Starting phenix.real_space_refine on Tue Sep 15 16:04:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5a0q_2981/09_2026/5a0q_2981.cif Found real_map, /net/cci-nas-00/data/ceres_data/5a0q_2981/09_2026/5a0q_2981.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5a0q_2981/09_2026/5a0q_2981.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5a0q_2981/09_2026/5a0q_2981.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5a0q_2981/09_2026/5a0q_2981.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5a0q_2981/09_2026/5a0q_2981.map" restraint_files = "/net/cci-nas-00/data/ceres_data/5a0q_2981/09_2026/5a0q_2981.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5a0q_2981/09_2026/5a0q_2981.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 284 5.16 5 C 27550 2.51 5 N 7448 2.21 5 O 8166 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 43448 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1514 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain breaks: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "B" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1671 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "C" Number of atoms: 1860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1860 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 5, 'TRANS': 231} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "D" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1674 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 6, 'TRANS': 207} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "E" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1643 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "F" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1535 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain breaks: 3 Chain: "G" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1626 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 5, 'TRANS': 203} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1372 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 4, 'TRANS': 178} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "I" Number of atoms: 1490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1490 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain breaks: 1 Chain: "J" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1374 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "K" Number of atoms: 1512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1512 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "L" Number of atoms: 1480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1480 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 2, 'TRANS': 189} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "M" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1453 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "N" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1428 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 5, 'TRANS': 178} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "O" Number of atoms: 1514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1514 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain breaks: 4 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "P" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1671 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 10, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Q" Number of atoms: 1860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 1860 Classifications: {'peptide': 237} Link IDs: {'PTRANS': 5, 'TRANS': 231} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "R" Number of atoms: 1674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1674 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 6, 'TRANS': 207} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "S" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1643 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "T" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1535 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 7, 'TRANS': 187} Chain breaks: 3 Chain: "U" Number of atoms: 1626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1626 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 5, 'TRANS': 203} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "V" Number of atoms: 1372 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1372 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 4, 'TRANS': 178} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "W" Number of atoms: 1490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1490 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 8, 'TRANS': 189} Chain breaks: 1 Chain: "X" Number of atoms: 1374 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1374 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain breaks: 3 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Y" Number of atoms: 1512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1512 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "Z" Number of atoms: 1480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1480 Classifications: {'peptide': 192} Link IDs: {'PTRANS': 2, 'TRANS': 189} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "a" Number of atoms: 1453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1453 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 5, 'TRANS': 184} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "b" Number of atoms: 1428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 1428 Classifications: {'peptide': 184} Link IDs: {'PTRANS': 5, 'TRANS': 178} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Chain: "H" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'KNM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'KNM:plan-4': 1, 'KNM:plan-5': 1, 'KNM:plan-6': 1} Unresolved non-hydrogen planarities: 15 Chain: "I" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'KNM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'KNM:plan-4': 1, 'KNM:plan-5': 1, 'KNM:plan-6': 1} Unresolved non-hydrogen planarities: 16 Chain: "L" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'KNM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'KNM:plan-4': 1, 'KNM:plan-5': 1, 'KNM:plan-6': 1} Unresolved non-hydrogen planarities: 15 Chain: "V" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'KNM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'KNM:plan-4': 1, 'KNM:plan-5': 1, 'KNM:plan-6': 1} Unresolved non-hydrogen planarities: 15 Chain: "W" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 30 Unusual residues: {'KNM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 27 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'KNM:plan-4': 1, 'KNM:plan-5': 1, 'KNM:plan-6': 1} Unresolved non-hydrogen planarities: 16 Chain: "Z" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'KNM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 26 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'KNM:plan-4': 1, 'KNM:plan-5': 1, 'KNM:plan-6': 1} Unresolved non-hydrogen planarities: 15 Time building chain proxies: 8.63, per 1000 atoms: 0.20 Number of scatterers: 43448 At special positions: 0 Unit cell: (132.08, 171.6, 134.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 284 16.00 O 8166 8.00 N 7448 7.00 C 27550 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS M 54 " - pdb=" SG CYS M 61 " distance=2.01 Simple disulfide: pdb=" SG CYS a 54 " - pdb=" SG CYS a 61 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=14, symmetry=0 Number of additional bonds: simple=14, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.36 Conformation dependent library (CDL) restraints added in 1.9 seconds 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10256 Finding SS restraints... Secondary structure from input PDB file: 138 helices and 0 sheets defined 35.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 23 through 35 Processing helix chain 'A' and resid 84 through 105 removed outlier: 4.026A pdb=" N ARG A 88 " --> pdb=" O THR A 84 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN A 90 " --> pdb=" O ASP A 86 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 127 removed outlier: 3.840A pdb=" N VAL A 124 " --> pdb=" O ASP A 120 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR A 125 " --> pdb=" O ILE A 121 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N THR A 126 " --> pdb=" O SER A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 181 removed outlier: 3.990A pdb=" N PHE A 178 " --> pdb=" O GLU A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 206 Processing helix chain 'A' and resid 212 through 214 No H-bonds generated for 'chain 'A' and resid 212 through 214' Processing helix chain 'B' and resid 19 through 29 Processing helix chain 'B' and resid 79 through 100 removed outlier: 3.788A pdb=" N ARG B 83 " --> pdb=" O GLY B 79 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL B 84 " --> pdb=" O PRO B 80 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N HIS B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 122 removed outlier: 4.147A pdb=" N TYR B 120 " --> pdb=" O VAL B 116 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N THR B 121 " --> pdb=" O MET B 117 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N GLN B 122 " --> pdb=" O GLN B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 166 through 176 removed outlier: 4.095A pdb=" N THR B 171 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 196 removed outlier: 3.760A pdb=" N THR B 189 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N GLU B 196 " --> pdb=" O LEU B 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 5 No H-bonds generated for 'chain 'C' and resid 3 through 5' Processing helix chain 'C' and resid 19 through 30 removed outlier: 3.679A pdb=" N ILE C 28 " --> pdb=" O ALA C 24 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY C 29 " --> pdb=" O MET C 25 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N HIS C 30 " --> pdb=" O GLU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 101 Processing helix chain 'C' and resid 107 through 123 removed outlier: 3.845A pdb=" N TYR C 121 " --> pdb=" O ILE C 117 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR C 122 " --> pdb=" O LYS C 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 178 removed outlier: 4.262A pdb=" N GLN C 177 " --> pdb=" O SER C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 186 through 200 Processing helix chain 'C' and resid 230 through 243 removed outlier: 3.719A pdb=" N GLU C 242 " --> pdb=" O LYS C 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 removed outlier: 3.732A pdb=" N LYS D 27 " --> pdb=" O GLN D 23 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS D 28 " --> pdb=" O GLU D 24 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 97 removed outlier: 4.639A pdb=" N ILE D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG D 86 " --> pdb=" O ILE D 82 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 119 removed outlier: 3.994A pdb=" N TYR D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N THR D 119 " --> pdb=" O LYS D 115 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 174 Processing helix chain 'D' and resid 185 through 198 removed outlier: 4.060A pdb=" N LEU D 195 " --> pdb=" O VAL D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 223 through 234 removed outlier: 4.565A pdb=" N LYS D 227 " --> pdb=" O GLU D 223 " (cutoff:3.500A) removed outlier: 5.574A pdb=" N TYR D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU D 231 " --> pdb=" O LYS D 227 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLU D 233 " --> pdb=" O VAL D 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 33 removed outlier: 3.937A pdb=" N LYS E 32 " --> pdb=" O ILE E 28 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU E 33 " --> pdb=" O GLU E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 103 removed outlier: 4.008A pdb=" N LYS E 86 " --> pdb=" O ILE E 82 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N THR E 87 " --> pdb=" O ALA E 83 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU E 88 " --> pdb=" O ASP E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 120 removed outlier: 3.775A pdb=" N VAL E 116 " --> pdb=" O VAL E 112 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N LEU E 119 " --> pdb=" O ALA E 115 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 184 removed outlier: 3.852A pdb=" N GLU E 183 " --> pdb=" O SER E 179 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL E 184 " --> pdb=" O SER E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 205 removed outlier: 3.513A pdb=" N SER E 198 " --> pdb=" O ALA E 194 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS E 203 " --> pdb=" O LEU E 199 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN E 204 " --> pdb=" O ILE E 200 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 235 removed outlier: 3.596A pdb=" N GLU E 235 " --> pdb=" O LYS E 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 231 through 235' Processing helix chain 'F' and resid 20 through 31 removed outlier: 3.777A pdb=" N GLU F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL F 29 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS F 30 " --> pdb=" O MET F 26 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLN F 31 " --> pdb=" O GLU F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 98 removed outlier: 3.774A pdb=" N GLN F 90 " --> pdb=" O ASN F 86 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER F 95 " --> pdb=" O GLU F 91 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 121 removed outlier: 4.206A pdb=" N ILE F 118 " --> pdb=" O SER F 114 " (cutoff:3.500A) Proline residue: F 119 - end of helix Processing helix chain 'F' and resid 165 through 174 removed outlier: 3.904A pdb=" N LEU F 172 " --> pdb=" O ALA F 168 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU F 173 " --> pdb=" O ARG F 169 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ARG F 174 " --> pdb=" O THR F 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 196 removed outlier: 3.681A pdb=" N ARG F 193 " --> pdb=" O LYS F 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 21 through 32 removed outlier: 3.847A pdb=" N ALA G 29 " --> pdb=" O TYR G 25 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N VAL G 30 " --> pdb=" O ALA G 26 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU G 31 " --> pdb=" O MET G 27 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 102 removed outlier: 4.122A pdb=" N SER G 86 " --> pdb=" O ALA G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 124 removed outlier: 3.893A pdb=" N ASP G 113 " --> pdb=" O LYS G 109 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TYR G 122 " --> pdb=" O TYR G 118 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N THR G 123 " --> pdb=" O VAL G 119 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU G 124 " --> pdb=" O HIS G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 178 Processing helix chain 'G' and resid 186 through 200 removed outlier: 4.550A pdb=" N LYS G 191 " --> pdb=" O ARG G 187 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA G 194 " --> pdb=" O VAL G 190 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 236 Processing helix chain 'H' and resid 49 through 54 removed outlier: 3.764A pdb=" N ALA H 54 " --> pdb=" O ALA H 50 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 70 removed outlier: 3.537A pdb=" N ILE H 68 " --> pdb=" O GLY H 64 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU H 69 " --> pdb=" O PHE H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 89 Processing helix chain 'H' and resid 132 through 140 removed outlier: 4.117A pdb=" N TYR H 136 " --> pdb=" O SER H 132 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLY H 137 " --> pdb=" O SER H 133 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N TYR H 138 " --> pdb=" O TYR H 134 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 166 removed outlier: 4.225A pdb=" N LEU H 153 " --> pdb=" O LYS H 149 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN H 154 " --> pdb=" O GLU H 150 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA H 161 " --> pdb=" O ALA H 157 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU H 162 " --> pdb=" O ASN H 158 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG H 166 " --> pdb=" O LEU H 162 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 70 Processing helix chain 'I' and resid 76 through 89 Processing helix chain 'I' and resid 130 through 141 removed outlier: 3.808A pdb=" N VAL I 137 " --> pdb=" O ALA I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 148 through 165 removed outlier: 4.510A pdb=" N LYS I 152 " --> pdb=" O GLU I 148 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN I 153 " --> pdb=" O GLU I 149 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER I 156 " --> pdb=" O LYS I 152 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLU I 157 " --> pdb=" O ASN I 153 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA I 158 " --> pdb=" O LEU I 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 76 removed outlier: 3.577A pdb=" N TYR J 73 " --> pdb=" O ARG J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 96 Processing helix chain 'J' and resid 159 through 176 removed outlier: 4.025A pdb=" N GLU J 164 " --> pdb=" O ASP J 160 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ARG J 176 " --> pdb=" O ASN J 172 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 71 removed outlier: 3.847A pdb=" N TYR K 59 " --> pdb=" O GLN K 55 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N ASN K 63 " --> pdb=" O TYR K 59 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS K 68 " --> pdb=" O VAL K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 77 through 93 removed outlier: 3.957A pdb=" N ARG K 93 " --> pdb=" O ALA K 89 " (cutoff:3.500A) Processing helix chain 'K' and resid 135 through 146 removed outlier: 5.303A pdb=" N SER K 141 " --> pdb=" O PHE K 137 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE K 142 " --> pdb=" O LEU K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 170 removed outlier: 3.541A pdb=" N VAL K 157 " --> pdb=" O ARG K 153 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU K 158 " --> pdb=" O GLU K 154 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS K 163 " --> pdb=" O LEU K 159 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU K 165 " --> pdb=" O ARG K 161 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU K 166 " --> pdb=" O LYS K 162 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N LEU K 167 " --> pdb=" O CYS K 163 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN K 168 " --> pdb=" O LEU K 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 70 removed outlier: 3.577A pdb=" N SER L 53 " --> pdb=" O ALA L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 76 through 90 removed outlier: 3.550A pdb=" N GLN L 89 " --> pdb=" O ASN L 85 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TYR L 90 " --> pdb=" O MET L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 142 removed outlier: 3.980A pdb=" N GLY L 137 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N VAL L 138 " --> pdb=" O TYR L 134 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG L 141 " --> pdb=" O GLY L 137 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY L 142 " --> pdb=" O VAL L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 166 removed outlier: 4.086A pdb=" N ARG L 166 " --> pdb=" O GLN L 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 58 through 79 removed outlier: 3.579A pdb=" N THR M 63 " --> pdb=" O GLY M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 98 removed outlier: 4.160A pdb=" N SER M 93 " --> pdb=" O ALA M 89 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N THR M 94 " --> pdb=" O ALA M 90 " (cutoff:3.500A) Processing helix chain 'M' and resid 142 through 153 Proline residue: M 147 - end of helix Processing helix chain 'M' and resid 168 through 185 removed outlier: 3.824A pdb=" N VAL M 178 " --> pdb=" O LEU M 174 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N PHE M 179 " --> pdb=" O VAL M 175 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 76 removed outlier: 3.829A pdb=" N LEU N 76 " --> pdb=" O ILE N 72 " (cutoff:3.500A) Processing helix chain 'N' and resid 85 through 102 removed outlier: 3.667A pdb=" N LYS N 102 " --> pdb=" O SER N 98 " (cutoff:3.500A) Processing helix chain 'N' and resid 146 through 156 removed outlier: 3.905A pdb=" N VAL N 153 " --> pdb=" O LEU N 149 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS N 156 " --> pdb=" O GLU N 152 " (cutoff:3.500A) Processing helix chain 'N' and resid 163 through 174 removed outlier: 4.057A pdb=" N ARG N 174 " --> pdb=" O GLU N 170 " (cutoff:3.500A) Processing helix chain 'O' and resid 23 through 35 Processing helix chain 'O' and resid 84 through 105 removed outlier: 4.026A pdb=" N ARG O 88 " --> pdb=" O THR O 84 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER O 89 " --> pdb=" O ALA O 85 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLN O 90 " --> pdb=" O ASP O 86 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS O 102 " --> pdb=" O ALA O 98 " (cutoff:3.500A) Processing helix chain 'O' and resid 111 through 127 removed outlier: 3.841A pdb=" N VAL O 124 " --> pdb=" O ASP O 120 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N TYR O 125 " --> pdb=" O ILE O 121 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR O 126 " --> pdb=" O SER O 122 " (cutoff:3.500A) Processing helix chain 'O' and resid 172 through 181 removed outlier: 3.990A pdb=" N PHE O 178 " --> pdb=" O GLU O 174 " (cutoff:3.500A) Processing helix chain 'O' and resid 194 through 206 Processing helix chain 'O' and resid 212 through 214 No H-bonds generated for 'chain 'O' and resid 212 through 214' Processing helix chain 'P' and resid 19 through 29 Processing helix chain 'P' and resid 79 through 100 removed outlier: 3.788A pdb=" N ARG P 83 " --> pdb=" O GLY P 79 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N VAL P 84 " --> pdb=" O PRO P 80 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N HIS P 87 " --> pdb=" O ARG P 83 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 122 removed outlier: 4.148A pdb=" N TYR P 120 " --> pdb=" O VAL P 116 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N THR P 121 " --> pdb=" O MET P 117 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLN P 122 " --> pdb=" O GLN P 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 166 through 176 removed outlier: 4.093A pdb=" N THR P 171 " --> pdb=" O VAL P 167 " (cutoff:3.500A) Processing helix chain 'P' and resid 183 through 196 removed outlier: 3.760A pdb=" N THR P 189 " --> pdb=" O ASP P 185 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA P 190 " --> pdb=" O ALA P 186 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLU P 196 " --> pdb=" O LEU P 192 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 5 No H-bonds generated for 'chain 'Q' and resid 3 through 5' Processing helix chain 'Q' and resid 19 through 30 removed outlier: 3.679A pdb=" N ILE Q 28 " --> pdb=" O ALA Q 24 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY Q 29 " --> pdb=" O MET Q 25 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N HIS Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 101 Processing helix chain 'Q' and resid 107 through 123 removed outlier: 3.845A pdb=" N TYR Q 121 " --> pdb=" O ILE Q 117 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR Q 122 " --> pdb=" O LYS Q 118 " (cutoff:3.500A) Processing helix chain 'Q' and resid 168 through 178 removed outlier: 4.262A pdb=" N GLN Q 177 " --> pdb=" O SER Q 173 " (cutoff:3.500A) Processing helix chain 'Q' and resid 186 through 200 Processing helix chain 'Q' and resid 230 through 243 removed outlier: 3.719A pdb=" N GLU Q 242 " --> pdb=" O LYS Q 238 " (cutoff:3.500A) Processing helix chain 'R' and resid 17 through 28 removed outlier: 3.732A pdb=" N LYS R 27 " --> pdb=" O GLN R 23 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS R 28 " --> pdb=" O GLU R 24 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 97 removed outlier: 4.639A pdb=" N ILE R 82 " --> pdb=" O ALA R 78 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ARG R 86 " --> pdb=" O ILE R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 119 removed outlier: 3.994A pdb=" N TYR R 118 " --> pdb=" O LEU R 114 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N THR R 119 " --> pdb=" O LYS R 115 " (cutoff:3.500A) Processing helix chain 'R' and resid 165 through 174 Processing helix chain 'R' and resid 185 through 198 removed outlier: 4.060A pdb=" N LEU R 195 " --> pdb=" O VAL R 191 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 234 removed outlier: 4.565A pdb=" N LYS R 227 " --> pdb=" O GLU R 223 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N TYR R 228 " --> pdb=" O GLU R 224 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N GLU R 231 " --> pdb=" O LYS R 227 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N GLU R 233 " --> pdb=" O VAL R 229 " (cutoff:3.500A) Processing helix chain 'S' and resid 22 through 33 removed outlier: 3.937A pdb=" N LYS S 32 " --> pdb=" O ILE S 28 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU S 33 " --> pdb=" O GLU S 29 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 103 removed outlier: 4.008A pdb=" N LYS S 86 " --> pdb=" O ILE S 82 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N THR S 87 " --> pdb=" O ALA S 83 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LEU S 88 " --> pdb=" O ASP S 84 " (cutoff:3.500A) Processing helix chain 'S' and resid 109 through 120 removed outlier: 3.775A pdb=" N VAL S 116 " --> pdb=" O VAL S 112 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU S 119 " --> pdb=" O ALA S 115 " (cutoff:3.500A) Processing helix chain 'S' and resid 174 through 184 removed outlier: 3.852A pdb=" N GLU S 183 " --> pdb=" O SER S 179 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL S 184 " --> pdb=" O SER S 180 " (cutoff:3.500A) Processing helix chain 'S' and resid 191 through 205 removed outlier: 3.512A pdb=" N SER S 198 " --> pdb=" O ALA S 194 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N LYS S 203 " --> pdb=" O LEU S 199 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLN S 204 " --> pdb=" O ILE S 200 " (cutoff:3.500A) Processing helix chain 'S' and resid 231 through 235 removed outlier: 3.596A pdb=" N GLU S 235 " --> pdb=" O LYS S 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 231 through 235' Processing helix chain 'T' and resid 20 through 31 removed outlier: 3.777A pdb=" N GLU T 27 " --> pdb=" O GLU T 23 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N VAL T 29 " --> pdb=" O ALA T 25 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LYS T 30 " --> pdb=" O MET T 26 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N GLN T 31 " --> pdb=" O GLU T 27 " (cutoff:3.500A) Processing helix chain 'T' and resid 78 through 98 removed outlier: 3.774A pdb=" N GLN T 90 " --> pdb=" O ASN T 86 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER T 95 " --> pdb=" O GLU T 91 " (cutoff:3.500A) Processing helix chain 'T' and resid 105 through 121 removed outlier: 4.207A pdb=" N ILE T 118 " --> pdb=" O SER T 114 " (cutoff:3.500A) Proline residue: T 119 - end of helix Processing helix chain 'T' and resid 165 through 174 removed outlier: 3.904A pdb=" N LEU T 172 " --> pdb=" O ALA T 168 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU T 173 " --> pdb=" O ARG T 169 " (cutoff:3.500A) removed outlier: 4.976A pdb=" N ARG T 174 " --> pdb=" O THR T 170 " (cutoff:3.500A) Processing helix chain 'T' and resid 184 through 196 removed outlier: 3.681A pdb=" N ARG T 193 " --> pdb=" O LYS T 189 " (cutoff:3.500A) Processing helix chain 'U' and resid 21 through 32 removed outlier: 3.848A pdb=" N ALA U 29 " --> pdb=" O TYR U 25 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N VAL U 30 " --> pdb=" O ALA U 26 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU U 31 " --> pdb=" O MET U 27 " (cutoff:3.500A) Processing helix chain 'U' and resid 81 through 102 removed outlier: 4.122A pdb=" N SER U 86 " --> pdb=" O ALA U 82 " (cutoff:3.500A) Processing helix chain 'U' and resid 108 through 124 removed outlier: 3.893A pdb=" N ASP U 113 " --> pdb=" O LYS U 109 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N TYR U 122 " --> pdb=" O TYR U 118 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N THR U 123 " --> pdb=" O VAL U 119 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N LEU U 124 " --> pdb=" O HIS U 120 " (cutoff:3.500A) Processing helix chain 'U' and resid 172 through 178 Processing helix chain 'U' and resid 186 through 200 removed outlier: 4.550A pdb=" N LYS U 191 " --> pdb=" O ARG U 187 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA U 194 " --> pdb=" O VAL U 190 " (cutoff:3.500A) Processing helix chain 'U' and resid 229 through 236 Processing helix chain 'V' and resid 49 through 54 removed outlier: 3.764A pdb=" N ALA V 54 " --> pdb=" O ALA V 50 " (cutoff:3.500A) Processing helix chain 'V' and resid 57 through 70 removed outlier: 3.537A pdb=" N ILE V 68 " --> pdb=" O GLY V 64 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N GLU V 69 " --> pdb=" O PHE V 65 " (cutoff:3.500A) Processing helix chain 'V' and resid 76 through 89 Processing helix chain 'V' and resid 132 through 140 removed outlier: 4.117A pdb=" N TYR V 136 " --> pdb=" O SER V 132 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N GLY V 137 " --> pdb=" O SER V 133 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N TYR V 138 " --> pdb=" O TYR V 134 " (cutoff:3.500A) Processing helix chain 'V' and resid 149 through 166 removed outlier: 4.225A pdb=" N LEU V 153 " --> pdb=" O LYS V 149 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN V 154 " --> pdb=" O GLU V 150 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ALA V 161 " --> pdb=" O ALA V 157 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU V 162 " --> pdb=" O ASN V 158 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ARG V 166 " --> pdb=" O LEU V 162 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 70 Processing helix chain 'W' and resid 76 through 89 Processing helix chain 'W' and resid 130 through 141 removed outlier: 3.808A pdb=" N VAL W 137 " --> pdb=" O ALA W 133 " (cutoff:3.500A) Processing helix chain 'W' and resid 148 through 165 removed outlier: 4.510A pdb=" N LYS W 152 " --> pdb=" O GLU W 148 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ASN W 153 " --> pdb=" O GLU W 149 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER W 156 " --> pdb=" O LYS W 152 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLU W 157 " --> pdb=" O ASN W 153 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ALA W 158 " --> pdb=" O LEU W 154 " (cutoff:3.500A) Processing helix chain 'X' and resid 56 through 76 removed outlier: 3.576A pdb=" N TYR X 73 " --> pdb=" O ARG X 69 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 96 Processing helix chain 'X' and resid 159 through 176 removed outlier: 4.025A pdb=" N GLU X 164 " --> pdb=" O ASP X 160 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARG X 176 " --> pdb=" O ASN X 172 " (cutoff:3.500A) Processing helix chain 'Y' and resid 51 through 71 removed outlier: 3.847A pdb=" N TYR Y 59 " --> pdb=" O GLN Y 55 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ASN Y 63 " --> pdb=" O TYR Y 59 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS Y 68 " --> pdb=" O VAL Y 64 " (cutoff:3.500A) Processing helix chain 'Y' and resid 77 through 93 removed outlier: 3.958A pdb=" N ARG Y 93 " --> pdb=" O ALA Y 89 " (cutoff:3.500A) Processing helix chain 'Y' and resid 135 through 146 removed outlier: 5.303A pdb=" N SER Y 141 " --> pdb=" O PHE Y 137 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE Y 142 " --> pdb=" O LEU Y 138 " (cutoff:3.500A) Processing helix chain 'Y' and resid 153 through 170 removed outlier: 3.541A pdb=" N VAL Y 157 " --> pdb=" O ARG Y 153 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N GLU Y 158 " --> pdb=" O GLU Y 154 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS Y 163 " --> pdb=" O LEU Y 159 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU Y 165 " --> pdb=" O ARG Y 161 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLU Y 166 " --> pdb=" O LYS Y 162 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU Y 167 " --> pdb=" O CYS Y 163 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLN Y 168 " --> pdb=" O LEU Y 164 " (cutoff:3.500A) Processing helix chain 'Z' and resid 49 through 70 removed outlier: 3.577A pdb=" N SER Z 53 " --> pdb=" O ALA Z 49 " (cutoff:3.500A) Processing helix chain 'Z' and resid 76 through 90 removed outlier: 3.550A pdb=" N GLN Z 89 " --> pdb=" O ASN Z 85 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TYR Z 90 " --> pdb=" O MET Z 86 " (cutoff:3.500A) Processing helix chain 'Z' and resid 132 through 142 removed outlier: 3.980A pdb=" N GLY Z 137 " --> pdb=" O VAL Z 133 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N VAL Z 138 " --> pdb=" O TYR Z 134 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ARG Z 141 " --> pdb=" O GLY Z 137 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLY Z 142 " --> pdb=" O VAL Z 138 " (cutoff:3.500A) Processing helix chain 'Z' and resid 149 through 166 removed outlier: 4.087A pdb=" N ARG Z 166 " --> pdb=" O GLN Z 162 " (cutoff:3.500A) Processing helix chain 'a' and resid 58 through 79 removed outlier: 3.579A pdb=" N THR a 63 " --> pdb=" O GLY a 59 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 98 removed outlier: 4.160A pdb=" N SER a 93 " --> pdb=" O ALA a 89 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N THR a 94 " --> pdb=" O ALA a 90 " (cutoff:3.500A) Processing helix chain 'a' and resid 142 through 153 Proline residue: a 147 - end of helix Processing helix chain 'a' and resid 168 through 185 removed outlier: 3.823A pdb=" N VAL a 178 " --> pdb=" O LEU a 174 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE a 179 " --> pdb=" O VAL a 175 " (cutoff:3.500A) Processing helix chain 'b' and resid 57 through 76 removed outlier: 3.829A pdb=" N LEU b 76 " --> pdb=" O ILE b 72 " (cutoff:3.500A) Processing helix chain 'b' and resid 85 through 102 removed outlier: 3.667A pdb=" N LYS b 102 " --> pdb=" O SER b 98 " (cutoff:3.500A) Processing helix chain 'b' and resid 146 through 156 removed outlier: 3.905A pdb=" N VAL b 153 " --> pdb=" O LEU b 149 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N LYS b 156 " --> pdb=" O GLU b 152 " (cutoff:3.500A) Processing helix chain 'b' and resid 163 through 174 removed outlier: 4.057A pdb=" N ARG b 174 " --> pdb=" O GLU b 170 " (cutoff:3.500A) 1202 hydrogen bonds defined for protein. 3606 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.93 Time building geometry restraints manager: 4.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 9099 1.33 - 1.46: 15127 1.46 - 1.59: 19485 1.59 - 1.72: 13 1.72 - 1.85: 450 Bond restraints: 44174 Sorted by residual: bond pdb=" C THR V 1 " pdb=" N THR V 2 " ideal model delta sigma weight residual 1.331 1.782 -0.451 1.30e-02 5.92e+03 1.20e+03 bond pdb=" C THR H 1 " pdb=" N THR H 2 " ideal model delta sigma weight residual 1.331 1.782 -0.451 1.30e-02 5.92e+03 1.20e+03 bond pdb=" C THR L 1 " pdb=" N THR L 2 " ideal model delta sigma weight residual 1.331 1.485 -0.154 1.37e-02 5.33e+03 1.27e+02 bond pdb=" C THR Z 1 " pdb=" N THR Z 2 " ideal model delta sigma weight residual 1.331 1.485 -0.154 1.37e-02 5.33e+03 1.27e+02 bond pdb=" N PRO I 123 " pdb=" CD PRO I 123 " ideal model delta sigma weight residual 1.473 1.367 0.106 1.40e-02 5.10e+03 5.72e+01 ... (remaining 44169 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.68: 59285 7.68 - 15.36: 309 15.36 - 23.03: 25 23.03 - 30.71: 2 30.71 - 38.39: 1 Bond angle restraints: 59622 Sorted by residual: angle pdb=" N GLY T 17 " pdb=" CA GLY T 17 " pdb=" C GLY T 17 " ideal model delta sigma weight residual 113.18 151.57 -38.39 2.37e+00 1.78e-01 2.62e+02 angle pdb=" N SER E 172 " pdb=" CA SER E 172 " pdb=" C SER E 172 " ideal model delta sigma weight residual 111.14 125.87 -14.73 1.08e+00 8.57e-01 1.86e+02 angle pdb=" N SER S 172 " pdb=" CA SER S 172 " pdb=" C SER S 172 " ideal model delta sigma weight residual 111.14 125.81 -14.67 1.08e+00 8.57e-01 1.84e+02 angle pdb=" N SER Q 153 " pdb=" CA SER Q 153 " pdb=" C SER Q 153 " ideal model delta sigma weight residual 108.79 89.26 19.53 1.53e+00 4.27e-01 1.63e+02 angle pdb=" N SER C 153 " pdb=" CA SER C 153 " pdb=" C SER C 153 " ideal model delta sigma weight residual 108.79 89.28 19.51 1.53e+00 4.27e-01 1.63e+02 ... (remaining 59617 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 23958 17.60 - 35.20: 1866 35.20 - 52.80: 391 52.80 - 70.41: 213 70.41 - 88.01: 72 Dihedral angle restraints: 26500 sinusoidal: 10464 harmonic: 16036 Sorted by residual: dihedral pdb=" CA GLU M 18 " pdb=" C GLU M 18 " pdb=" N ASP M 19 " pdb=" CA ASP M 19 " ideal model delta harmonic sigma weight residual 180.00 -137.66 -42.34 0 5.00e+00 4.00e-02 7.17e+01 dihedral pdb=" CA GLU a 18 " pdb=" C GLU a 18 " pdb=" N ASP a 19 " pdb=" CA ASP a 19 " ideal model delta harmonic sigma weight residual -180.00 -137.66 -42.34 0 5.00e+00 4.00e-02 7.17e+01 dihedral pdb=" C GLN V 7 " pdb=" N GLN V 7 " pdb=" CA GLN V 7 " pdb=" CB GLN V 7 " ideal model delta harmonic sigma weight residual -122.60 -103.78 -18.82 0 2.50e+00 1.60e-01 5.67e+01 ... (remaining 26497 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.144: 5441 0.144 - 0.288: 1168 0.288 - 0.433: 102 0.433 - 0.577: 20 0.577 - 0.721: 1 Chirality restraints: 6732 Sorted by residual: chirality pdb=" CA PHE H 8 " pdb=" N PHE H 8 " pdb=" C PHE H 8 " pdb=" CB PHE H 8 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" CA MET W 135 " pdb=" N MET W 135 " pdb=" C MET W 135 " pdb=" CB MET W 135 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.31e+00 chirality pdb=" CA MET I 135 " pdb=" N MET I 135 " pdb=" C MET I 135 " pdb=" CB MET I 135 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.31e+00 ... (remaining 6729 not shown) Planarity restraints: 7614 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C3 KNM W 300 " 0.005 2.00e-02 2.50e+03 2.67e-01 8.94e+02 pdb=" C8 KNM W 300 " -0.068 2.00e-02 2.50e+03 pdb=" C9 KNM W 300 " 0.312 2.00e-02 2.50e+03 pdb=" N2 KNM W 300 " -0.460 2.00e-02 2.50e+03 pdb=" O3 KNM W 300 " 0.211 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 KNM I 300 " -0.005 2.00e-02 2.50e+03 2.67e-01 8.93e+02 pdb=" C8 KNM I 300 " 0.068 2.00e-02 2.50e+03 pdb=" C9 KNM I 300 " -0.311 2.00e-02 2.50e+03 pdb=" N2 KNM I 300 " 0.460 2.00e-02 2.50e+03 pdb=" O3 KNM I 300 " -0.211 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C3 KNM H 300 " -0.191 2.00e-02 2.50e+03 2.47e-01 7.65e+02 pdb=" C8 KNM H 300 " 0.082 2.00e-02 2.50e+03 pdb=" C9 KNM H 300 " -0.298 2.00e-02 2.50e+03 pdb=" N2 KNM H 300 " 0.417 2.00e-02 2.50e+03 pdb=" O3 KNM H 300 " -0.010 2.00e-02 2.50e+03 ... (remaining 7611 not shown) Histogram of nonbonded interaction distances: 0.70 - 1.54: 8 1.54 - 2.38: 298 2.38 - 3.22: 44308 3.22 - 4.06: 114887 4.06 - 4.90: 213821 Warning: very small nonbonded interaction distances. Nonbonded interactions: 373322 Sorted by model distance: nonbonded pdb=" O SER Y 23 " pdb=" OD1 ASN Y 24 " model vdw 0.702 3.040 nonbonded pdb=" O SER K 23 " pdb=" OD1 ASN K 24 " model vdw 0.702 3.040 nonbonded pdb=" O VAL X 137 " pdb=" OH TYR X 146 " model vdw 0.977 3.040 nonbonded pdb=" O VAL J 137 " pdb=" OH TYR J 146 " model vdw 0.977 3.040 nonbonded pdb=" ND2 ASN V 28 " pdb=" OG1 THR V 31 " model vdw 1.432 3.120 ... (remaining 373317 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'Q' } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'S' } ncs_group { reference = chain 'F' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'W' } ncs_group { reference = chain 'J' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'Z' } ncs_group { reference = chain 'M' selection = chain 'a' } ncs_group { reference = chain 'N' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.810 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 33.190 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6085 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.020 0.451 44190 Z= 1.413 Angle : 2.216 38.391 59626 Z= 1.459 Chirality : 0.115 0.721 6732 Planarity : 0.019 0.267 7614 Dihedral : 15.416 88.008 16238 Min Nonbonded Distance : 0.702 Molprobity Statistics. All-atom Clashscore : 33.76 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.46 % Favored : 95.14 % Rotamer: Outliers : 1.99 % Allowed : 9.50 % Favored : 88.51 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.18 (0.09), residues: 5432 helix: -2.12 (0.08), residues: 1892 sheet: -2.40 (0.13), residues: 1204 loop : -1.71 (0.12), residues: 2336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG U 129 TYR 0.135 0.018 TYR M 188 PHE 0.115 0.015 PHE Z 6 TRP 0.105 0.015 TRP V 103 HIS 0.008 0.001 HIS T 43 Details of bonding type rmsd/Z covalent geometry : bond 0.01928 / 1.35 (44174) covalent geometry : angle 2.21575 / 1.46 (59622) SS BOND : bond 0.02364 / 1.19 ( 2) SS BOND : angle 4.12377 / 2.23 ( 4) hydrogen bonds : bond 0.19765 / 13.20 ( 1202) hydrogen bonds : angle 8.40085 / 5.92 ( 3606) Misc. bond : bond 0.23237 / 11.43 ( 14) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1964 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 1872 time to evaluate : 2.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 237 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR J 196 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU M 205 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS U 237 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR X 196 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU a 205 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 32 ILE cc_start: 0.7694 (mt) cc_final: 0.7369 (mt) REVERT: B 51 GLN cc_start: 0.3954 (OUTLIER) cc_final: 0.2828 (pp30) REVERT: B 207 ILE cc_start: 0.5425 (OUTLIER) cc_final: 0.5213 (pp) REVERT: B 213 ASN cc_start: 0.6666 (OUTLIER) cc_final: 0.6249 (m-40) REVERT: D 153 TYR cc_start: 0.7335 (p90) cc_final: 0.7116 (p90) REVERT: E 21 LEU cc_start: 0.6570 (mt) cc_final: 0.6313 (mp) REVERT: E 70 ILE cc_start: 0.8619 (OUTLIER) cc_final: 0.8326 (mm) REVERT: E 97 GLN cc_start: 0.8430 (mm-40) cc_final: 0.8166 (mm110) REVERT: H 186 ARG cc_start: 0.6253 (OUTLIER) cc_final: 0.5123 (mtt180) REVERT: I 126 THR cc_start: 0.8573 (p) cc_final: 0.8157 (m) REVERT: I 139 GLU cc_start: 0.5315 (tt0) cc_final: 0.5106 (tt0) REVERT: J 134 ASP cc_start: 0.5606 (p0) cc_final: 0.5213 (p0) REVERT: J 170 MET cc_start: 0.7280 (tpt) cc_final: 0.7007 (tpt) REVERT: K 14 LEU cc_start: 0.7694 (tp) cc_final: 0.7233 (tt) REVERT: M 15 ILE cc_start: 0.5411 (OUTLIER) cc_final: 0.5143 (pt) REVERT: M 28 ARG cc_start: 0.5771 (ptt180) cc_final: 0.5282 (ptm160) REVERT: M 72 LEU cc_start: 0.7819 (pp) cc_final: 0.7538 (pp) REVERT: M 74 MET cc_start: 0.6047 (mtt) cc_final: 0.5773 (mtp) REVERT: M 173 ARG cc_start: 0.4914 (tpp-160) cc_final: 0.4587 (mtp85) REVERT: N 199 ILE cc_start: 0.5885 (mt) cc_final: 0.5662 (mp) REVERT: O 32 ILE cc_start: 0.7672 (mt) cc_final: 0.7345 (mt) REVERT: O 104 LYS cc_start: 0.7686 (mtpt) cc_final: 0.7328 (mtpt) REVERT: P 51 GLN cc_start: 0.3948 (OUTLIER) cc_final: 0.2819 (pp30) REVERT: P 207 ILE cc_start: 0.5425 (OUTLIER) cc_final: 0.5217 (pp) REVERT: P 213 ASN cc_start: 0.6668 (OUTLIER) cc_final: 0.6250 (m-40) REVERT: R 153 TYR cc_start: 0.7356 (p90) cc_final: 0.7130 (p90) REVERT: S 21 LEU cc_start: 0.6623 (mt) cc_final: 0.6382 (mp) REVERT: S 70 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.8313 (mm) REVERT: S 97 GLN cc_start: 0.8464 (mm-40) cc_final: 0.8202 (mm110) REVERT: V 186 ARG cc_start: 0.6294 (OUTLIER) cc_final: 0.5139 (mtt180) REVERT: W 24 MET cc_start: 0.5937 (mmt) cc_final: 0.5627 (mmt) REVERT: W 126 THR cc_start: 0.8592 (p) cc_final: 0.8171 (m) REVERT: W 139 GLU cc_start: 0.5309 (tt0) cc_final: 0.5106 (tt0) REVERT: X 134 ASP cc_start: 0.5616 (p0) cc_final: 0.5222 (p0) REVERT: X 170 MET cc_start: 0.7293 (tpt) cc_final: 0.7033 (tpt) REVERT: Y 14 LEU cc_start: 0.7678 (tp) cc_final: 0.7217 (tt) REVERT: a 15 ILE cc_start: 0.5396 (OUTLIER) cc_final: 0.5110 (pt) REVERT: a 28 ARG cc_start: 0.5748 (ptt180) cc_final: 0.5271 (ptm160) REVERT: a 72 LEU cc_start: 0.7828 (pp) cc_final: 0.7545 (pp) REVERT: a 74 MET cc_start: 0.6053 (mtt) cc_final: 0.5803 (mtp) REVERT: a 173 ARG cc_start: 0.4951 (tpp-160) cc_final: 0.4570 (mtp85) outliers start: 92 outliers final: 30 residues processed: 1930 average time/residue: 0.2712 time to fit residues: 834.8463 Evaluate side-chains 1439 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 1397 time to evaluate : 1.195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 229 ILE Chi-restraints excluded: chain B residue 51 GLN Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 207 ILE Chi-restraints excluded: chain B residue 213 ASN Chi-restraints excluded: chain B residue 222 PRO Chi-restraints excluded: chain C residue 41 ASP Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 26 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain E residue 70 ILE Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 186 ARG Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain K residue 100 VAL Chi-restraints excluded: chain M residue 15 ILE Chi-restraints excluded: chain N residue 21 VAL Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 229 ILE Chi-restraints excluded: chain P residue 51 GLN Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 70 HIS Chi-restraints excluded: chain P residue 140 GLU Chi-restraints excluded: chain P residue 207 ILE Chi-restraints excluded: chain P residue 213 ASN Chi-restraints excluded: chain P residue 222 PRO Chi-restraints excluded: chain Q residue 41 ASP Chi-restraints excluded: chain Q residue 203 VAL Chi-restraints excluded: chain R residue 26 VAL Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain V residue 6 VAL Chi-restraints excluded: chain V residue 186 ARG Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain Y residue 100 VAL Chi-restraints excluded: chain a residue 15 ILE Chi-restraints excluded: chain b residue 21 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 394 optimal weight: 8.9990 chunk 430 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 265 optimal weight: 0.9980 chunk 523 optimal weight: 1.9990 chunk 497 optimal weight: 2.9990 chunk 414 optimal weight: 1.9990 chunk 310 optimal weight: 0.4980 chunk 488 optimal weight: 3.9990 chunk 366 optimal weight: 3.9990 chunk 223 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 ASN A 68 HIS A 90 GLN B 51 GLN B 62 HIS B 87 HIS ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN ** B 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 ASN C 142 HIS C 166 ASN D 54 GLN E 155 HIS E 224 GLN F 43 HIS ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 7 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 GLN H 110 GLN H 154 GLN ** I 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 GLN ** J 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 187 HIS L 162 GLN N 104 ASN N 108 ASN N 147 GLN O 33 ASN O 68 HIS O 90 GLN P 51 GLN P 62 HIS P 87 HIS ** P 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 206 ASN ** P 213 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 69 ASN Q 142 HIS Q 166 ASN R 54 GLN S 155 HIS S 224 GLN T 20 HIS T 43 HIS T 166 GLN ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 110 HIS ** V 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 62 GLN V 110 GLN V 154 GLN ** W 62 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 85 GLN ** X 6 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 187 HIS ** Y 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 162 GLN b 104 ASN b 108 ASN b 147 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.199105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.193711 restraints weight = 70630.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.194908 restraints weight = 47276.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.195816 restraints weight = 32861.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.196388 restraints weight = 24284.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.196828 restraints weight = 18731.693| |-----------------------------------------------------------------------------| r_work (final): 0.4326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6241 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 44190 Z= 0.171 Angle : 0.785 16.355 59626 Z= 0.415 Chirality : 0.048 0.241 6732 Planarity : 0.007 0.174 7614 Dihedral : 7.441 77.916 6194 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.72 % Favored : 97.18 % Rotamer: Outliers : 4.29 % Allowed : 16.37 % Favored : 79.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.10), residues: 5432 helix: -0.75 (0.10), residues: 1936 sheet: -2.16 (0.13), residues: 1292 loop : -1.36 (0.13), residues: 2204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.055 0.001 ARG N 186 TYR 0.028 0.002 TYR Z 88 PHE 0.036 0.002 PHE X 116 TRP 0.019 0.002 TRP N 91 HIS 0.009 0.002 HIS H 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.17 (44174) covalent geometry : angle 0.78537 / 0.41 (59622) SS BOND : bond 0.00504 / 0.25 ( 2) SS BOND : angle 1.80241 / 1.24 ( 4) hydrogen bonds : bond 0.04982 / 3.27 ( 1202) hydrogen bonds : angle 5.11206 / 3.60 ( 3606) Misc. bond : bond 0.00533 / 0.27 ( 14) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1755 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 1557 time to evaluate : 1.602 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 237 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR J 196 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLU M 205 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS U 237 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "THR X 196 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU a 205 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: B 94 GLN cc_start: 0.7043 (mm110) cc_final: 0.6811 (mm-40) REVERT: B 96 TYR cc_start: 0.7219 (t80) cc_final: 0.6664 (t80) REVERT: C 116 ASP cc_start: 0.7387 (m-30) cc_final: 0.7170 (m-30) REVERT: C 119 GLN cc_start: 0.6249 (tp-100) cc_final: 0.5938 (tp-100) REVERT: D 94 HIS cc_start: 0.8253 (t-90) cc_final: 0.7862 (t-90) REVERT: D 153 TYR cc_start: 0.7590 (p90) cc_final: 0.7269 (p90) REVERT: D 233 GLU cc_start: 0.5193 (mt-10) cc_final: 0.4692 (mm-30) REVERT: E 86 LYS cc_start: 0.7270 (ttpt) cc_final: 0.6841 (mtpt) REVERT: F 180 MET cc_start: 0.4850 (mmm) cc_final: 0.3720 (mtm) REVERT: G 167 LYS cc_start: 0.6422 (OUTLIER) cc_final: 0.6108 (pttt) REVERT: H 92 GLU cc_start: 0.6397 (pm20) cc_final: 0.6000 (pm20) REVERT: H 122 ARG cc_start: 0.7503 (ttt180) cc_final: 0.6746 (tmt170) REVERT: H 142 THR cc_start: 0.7235 (m) cc_final: 0.5667 (p) REVERT: I 65 LEU cc_start: 0.7471 (mt) cc_final: 0.7220 (mt) REVERT: J 93 LEU cc_start: 0.8068 (tp) cc_final: 0.7847 (tt) REVERT: K 14 LEU cc_start: 0.7357 (tp) cc_final: 0.7100 (tt) REVERT: K 119 ASP cc_start: 0.7651 (OUTLIER) cc_final: 0.7285 (t70) REVERT: L 19 ARG cc_start: 0.7388 (ttm170) cc_final: 0.7089 (ttt180) REVERT: L 42 LEU cc_start: 0.6469 (mt) cc_final: 0.5770 (tp) REVERT: L 57 ARG cc_start: 0.7393 (mtp85) cc_final: 0.7191 (mtp180) REVERT: L 143 TYR cc_start: 0.6520 (t80) cc_final: 0.5809 (t80) REVERT: M 28 ARG cc_start: 0.5746 (ptt180) cc_final: 0.4882 (ptm160) REVERT: M 72 LEU cc_start: 0.8286 (pp) cc_final: 0.8025 (pp) REVERT: P 94 GLN cc_start: 0.6994 (mm110) cc_final: 0.6732 (mm-40) REVERT: P 96 TYR cc_start: 0.7196 (t80) cc_final: 0.6660 (t80) REVERT: Q 116 ASP cc_start: 0.7357 (m-30) cc_final: 0.7134 (m-30) REVERT: Q 119 GLN cc_start: 0.6252 (tp-100) cc_final: 0.5949 (tp-100) REVERT: R 94 HIS cc_start: 0.8272 (t-90) cc_final: 0.7897 (t-90) REVERT: R 153 TYR cc_start: 0.7589 (p90) cc_final: 0.7266 (p90) REVERT: R 233 GLU cc_start: 0.5185 (mt-10) cc_final: 0.4697 (mm-30) REVERT: S 86 LYS cc_start: 0.7260 (ttpt) cc_final: 0.6829 (mtpt) REVERT: T 16 GLN cc_start: 0.5255 (OUTLIER) cc_final: 0.4423 (mp10) REVERT: T 180 MET cc_start: 0.4874 (mmm) cc_final: 0.3721 (mtm) REVERT: U 167 LYS cc_start: 0.6436 (OUTLIER) cc_final: 0.6106 (pttt) REVERT: V 70 LEU cc_start: 0.8005 (mp) cc_final: 0.7624 (mp) REVERT: V 72 GLU cc_start: 0.5238 (mt-10) cc_final: 0.5026 (mt-10) REVERT: V 92 GLU cc_start: 0.6395 (pm20) cc_final: 0.5991 (pm20) REVERT: V 142 THR cc_start: 0.7076 (m) cc_final: 0.5537 (p) REVERT: Y 14 LEU cc_start: 0.7355 (tp) cc_final: 0.7097 (tt) REVERT: Y 119 ASP cc_start: 0.7673 (OUTLIER) cc_final: 0.7323 (t70) REVERT: Z 19 ARG cc_start: 0.7399 (ttm170) cc_final: 0.7100 (ttt180) REVERT: Z 42 LEU cc_start: 0.6477 (mt) cc_final: 0.5776 (tp) REVERT: Z 143 TYR cc_start: 0.6532 (t80) cc_final: 0.5810 (t80) REVERT: a 72 LEU cc_start: 0.8299 (pp) cc_final: 0.8041 (pp) REVERT: a 173 ARG cc_start: 0.5595 (tpp-160) cc_final: 0.4763 (mtp180) outliers start: 198 outliers final: 104 residues processed: 1668 average time/residue: 0.2702 time to fit residues: 722.3827 Evaluate side-chains 1455 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 1346 time to evaluate : 1.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 221 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 43 LEU Chi-restraints excluded: chain D residue 71 MET Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 227 HIS Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 167 LYS Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 220 THR Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 192 ASP Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 119 ASP Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 141 ARG Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 147 GLN Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain N residue 193 THR Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 159 TYR Chi-restraints excluded: chain O residue 207 SER Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 70 HIS Chi-restraints excluded: chain P residue 133 LEU Chi-restraints excluded: chain P residue 212 CYS Chi-restraints excluded: chain P residue 221 THR Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 133 SER Chi-restraints excluded: chain Q residue 203 VAL Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 71 MET Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 220 VAL Chi-restraints excluded: chain S residue 227 HIS Chi-restraints excluded: chain T residue 16 GLN Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 114 SER Chi-restraints excluded: chain U residue 90 ILE Chi-restraints excluded: chain U residue 167 LYS Chi-restraints excluded: chain U residue 199 ILE Chi-restraints excluded: chain U residue 220 THR Chi-restraints excluded: chain V residue 6 VAL Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain W residue 125 VAL Chi-restraints excluded: chain X residue 90 VAL Chi-restraints excluded: chain X residue 192 ASP Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 119 ASP Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 51 ASP Chi-restraints excluded: chain Z residue 74 ILE Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain Z residue 125 THR Chi-restraints excluded: chain Z residue 141 ARG Chi-restraints excluded: chain a residue 29 LEU Chi-restraints excluded: chain a residue 175 VAL Chi-restraints excluded: chain b residue 130 VAL Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 147 GLN Chi-restraints excluded: chain b residue 169 VAL Chi-restraints excluded: chain b residue 191 THR Chi-restraints excluded: chain b residue 193 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 240 optimal weight: 0.0770 chunk 443 optimal weight: 1.9990 chunk 531 optimal weight: 9.9990 chunk 392 optimal weight: 10.0000 chunk 344 optimal weight: 10.0000 chunk 347 optimal weight: 7.9990 chunk 534 optimal weight: 5.9990 chunk 247 optimal weight: 0.0060 chunk 318 optimal weight: 5.9990 chunk 188 optimal weight: 1.9990 chunk 452 optimal weight: 7.9990 overall best weight: 2.0160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 ASN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN B 168 ASN E 178 GLN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 GLN K 65 GLN L 162 GLN M 108 ASN M 131 GLN N 61 GLN N 104 ASN O 33 ASN ** P 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 108 GLN P 168 ASN S 178 GLN ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 62 GLN Y 65 GLN Z 162 GLN a 108 ASN a 131 GLN b 61 GLN b 104 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.193585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.187323 restraints weight = 73158.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.188887 restraints weight = 44851.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.189937 restraints weight = 29805.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.190696 restraints weight = 20991.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.191250 restraints weight = 15509.316| |-----------------------------------------------------------------------------| r_work (final): 0.4324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6255 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 44190 Z= 0.153 Angle : 0.698 13.925 59626 Z= 0.365 Chirality : 0.046 0.198 6732 Planarity : 0.006 0.186 7614 Dihedral : 6.563 59.811 6132 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.39 % Favored : 96.52 % Rotamer: Outliers : 5.36 % Allowed : 18.47 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.11), residues: 5432 helix: -0.35 (0.11), residues: 1960 sheet: -2.07 (0.13), residues: 1270 loop : -1.27 (0.13), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.042 0.001 ARG N 186 TYR 0.027 0.002 TYR Z 136 PHE 0.031 0.002 PHE F 97 TRP 0.016 0.002 TRP X 153 HIS 0.009 0.001 HIS H 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 (44174) covalent geometry : angle 0.69805 / 0.36 (59622) SS BOND : bond 0.00316 / 0.16 ( 2) SS BOND : angle 1.79684 / 1.13 ( 4) hydrogen bonds : bond 0.04470 / 2.98 ( 1202) hydrogen bonds : angle 4.76444 / 3.35 ( 3606) Misc. bond : bond 0.00561 / 0.26 ( 14) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1679 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 247 poor density : 1432 time to evaluate : 1.734 Fit side-chains TARDY: cannot create tardy model for: "ILE A 235 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS G 237 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU M 205 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE O 235 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "LYS U 237 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU a 205 " (corrupted residue). Skipping it. revert: symmetry clash REVERT: A 76 ILE cc_start: 0.7259 (OUTLIER) cc_final: 0.6648 (mp) REVERT: B 94 GLN cc_start: 0.6844 (mm110) cc_final: 0.6577 (mm-40) REVERT: B 96 TYR cc_start: 0.6770 (t80) cc_final: 0.6428 (t80) REVERT: B 217 PHE cc_start: 0.5343 (t80) cc_final: 0.5081 (t80) REVERT: C 12 PHE cc_start: 0.7648 (OUTLIER) cc_final: 0.7309 (m-80) REVERT: C 119 GLN cc_start: 0.6234 (tp-100) cc_final: 0.5878 (tp-100) REVERT: D 94 HIS cc_start: 0.8051 (t-90) cc_final: 0.7646 (t-90) REVERT: D 153 TYR cc_start: 0.7504 (p90) cc_final: 0.7263 (p90) REVERT: E 51 GLU cc_start: 0.5861 (OUTLIER) cc_final: 0.5653 (tm-30) REVERT: E 86 LYS cc_start: 0.7195 (ttpt) cc_final: 0.6785 (mtpt) REVERT: F 77 LEU cc_start: 0.6078 (OUTLIER) cc_final: 0.5874 (pp) REVERT: G 167 LYS cc_start: 0.6365 (OUTLIER) cc_final: 0.6011 (pttt) REVERT: H 127 ILE cc_start: 0.6898 (OUTLIER) cc_final: 0.6697 (pt) REVERT: I 82 MET cc_start: 0.6381 (ptt) cc_final: 0.6053 (ptt) REVERT: L 42 LEU cc_start: 0.7053 (mt) cc_final: 0.6727 (mt) REVERT: L 51 ASP cc_start: 0.6317 (OUTLIER) cc_final: 0.6075 (t0) REVERT: L 74 ILE cc_start: 0.7237 (OUTLIER) cc_final: 0.6840 (tt) REVERT: L 143 TYR cc_start: 0.6756 (t80) cc_final: 0.6249 (t80) REVERT: M 28 ARG cc_start: 0.5680 (ptt180) cc_final: 0.4912 (ptm160) REVERT: M 91 MET cc_start: 0.6711 (ppp) cc_final: 0.6123 (ptm) REVERT: M 148 LEU cc_start: 0.5102 (tt) cc_final: 0.4428 (tp) REVERT: M 168 LEU cc_start: 0.5337 (mp) cc_final: 0.4915 (tp) REVERT: N 38 ASN cc_start: 0.5914 (t0) cc_final: 0.5404 (t0) REVERT: N 76 LEU cc_start: 0.6358 (OUTLIER) cc_final: 0.6003 (pp) REVERT: O 76 ILE cc_start: 0.7230 (OUTLIER) cc_final: 0.6630 (mp) REVERT: P 94 GLN cc_start: 0.6883 (mm110) cc_final: 0.6652 (mm-40) REVERT: P 96 TYR cc_start: 0.6763 (t80) cc_final: 0.6422 (t80) REVERT: P 217 PHE cc_start: 0.5351 (t80) cc_final: 0.5096 (t80) REVERT: Q 12 PHE cc_start: 0.7641 (OUTLIER) cc_final: 0.7305 (m-80) REVERT: Q 119 GLN cc_start: 0.6308 (tp-100) cc_final: 0.5950 (tp-100) REVERT: R 94 HIS cc_start: 0.8027 (t-90) cc_final: 0.7598 (t-90) REVERT: R 153 TYR cc_start: 0.7500 (p90) cc_final: 0.7272 (p90) REVERT: S 51 GLU cc_start: 0.5857 (OUTLIER) cc_final: 0.5637 (tm-30) REVERT: S 86 LYS cc_start: 0.7187 (ttpt) cc_final: 0.6800 (mtpt) REVERT: T 6 TYR cc_start: 0.4191 (t80) cc_final: 0.3940 (t80) REVERT: T 16 GLN cc_start: 0.5044 (OUTLIER) cc_final: 0.4106 (mp10) REVERT: T 18 ARG cc_start: 0.5699 (mpp-170) cc_final: 0.5001 (mpt90) REVERT: T 77 LEU cc_start: 0.6079 (OUTLIER) cc_final: 0.5878 (pp) REVERT: U 167 LYS cc_start: 0.6356 (OUTLIER) cc_final: 0.6013 (pttt) REVERT: W 82 MET cc_start: 0.6597 (ptt) cc_final: 0.6265 (ptt) REVERT: W 135 MET cc_start: 0.6435 (mmm) cc_final: 0.6188 (mmm) REVERT: Z 42 LEU cc_start: 0.7068 (mt) cc_final: 0.6720 (mt) REVERT: Z 51 ASP cc_start: 0.6290 (OUTLIER) cc_final: 0.6050 (t0) REVERT: Z 74 ILE cc_start: 0.7204 (OUTLIER) cc_final: 0.6836 (tt) REVERT: Z 143 TYR cc_start: 0.6753 (t80) cc_final: 0.6256 (t80) REVERT: a 91 MET cc_start: 0.6689 (ppp) cc_final: 0.6082 (ptm) REVERT: a 148 LEU cc_start: 0.5085 (tt) cc_final: 0.4392 (tp) REVERT: a 168 LEU cc_start: 0.5366 (mp) cc_final: 0.4958 (tp) REVERT: a 173 ARG cc_start: 0.5271 (tpp-160) cc_final: 0.4549 (mtp180) REVERT: b 38 ASN cc_start: 0.5887 (t0) cc_final: 0.5422 (t0) REVERT: b 76 LEU cc_start: 0.6358 (OUTLIER) cc_final: 0.5997 (pp) outliers start: 247 outliers final: 135 residues processed: 1571 average time/residue: 0.2660 time to fit residues: 672.4758 Evaluate side-chains 1470 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 153 poor density : 1317 time to evaluate : 1.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 95 ARG Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 51 GLU Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 167 LYS Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 8 PHE Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain H residue 127 ILE Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 192 ASP Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 73 TYR Chi-restraints excluded: chain K residue 119 ASP Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 84 THR Chi-restraints excluded: chain O residue 159 TYR Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 207 SER Chi-restraints excluded: chain O residue 235 ILE Chi-restraints excluded: chain P residue 47 THR Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 70 HIS Chi-restraints excluded: chain P residue 133 LEU Chi-restraints excluded: chain P residue 212 CYS Chi-restraints excluded: chain Q residue 12 PHE Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 100 GLN Chi-restraints excluded: chain Q residue 133 SER Chi-restraints excluded: chain Q residue 203 VAL Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 95 ARG Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 141 THR Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 51 GLU Chi-restraints excluded: chain S residue 114 GLN Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 179 SER Chi-restraints excluded: chain S residue 215 ILE Chi-restraints excluded: chain T residue 16 GLN Chi-restraints excluded: chain T residue 20 HIS Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 114 SER Chi-restraints excluded: chain U residue 32 ASN Chi-restraints excluded: chain U residue 35 THR Chi-restraints excluded: chain U residue 70 ASP Chi-restraints excluded: chain U residue 90 ILE Chi-restraints excluded: chain U residue 167 LYS Chi-restraints excluded: chain U residue 199 ILE Chi-restraints excluded: chain V residue 6 VAL Chi-restraints excluded: chain V residue 8 PHE Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 121 VAL Chi-restraints excluded: chain V residue 169 SER Chi-restraints excluded: chain V residue 174 ILE Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 32 SER Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain W residue 125 VAL Chi-restraints excluded: chain W residue 132 LEU Chi-restraints excluded: chain W residue 186 LEU Chi-restraints excluded: chain X residue 55 LEU Chi-restraints excluded: chain X residue 90 VAL Chi-restraints excluded: chain X residue 192 ASP Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 73 TYR Chi-restraints excluded: chain Y residue 119 ASP Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 51 ASP Chi-restraints excluded: chain Z residue 74 ILE Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain Z residue 125 THR Chi-restraints excluded: chain Z residue 138 VAL Chi-restraints excluded: chain a residue 29 LEU Chi-restraints excluded: chain a residue 175 VAL Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 130 VAL Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 169 VAL Chi-restraints excluded: chain b residue 191 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 444 optimal weight: 4.9990 chunk 402 optimal weight: 6.9990 chunk 394 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 515 optimal weight: 1.9990 chunk 139 optimal weight: 2.9990 chunk 528 optimal weight: 4.9990 chunk 133 optimal weight: 2.9990 chunk 352 optimal weight: 8.9990 chunk 538 optimal weight: 6.9990 chunk 43 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 33 ASN A 75 ASN ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 154 HIS E 155 HIS E 224 GLN F 20 HIS F 69 HIS ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 GLN I 85 GLN J 6 ASN N 104 ASN O 33 ASN O 75 ASN ** P 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 102 GLN R 154 HIS ** R 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 155 HIS S 224 GLN T 69 HIS T 166 GLN ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 110 HIS ** V 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 62 GLN W 85 GLN X 6 ASN b 104 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4301 r_free = 0.4301 target = 0.192112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.186121 restraints weight = 73437.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4250 r_free = 0.4250 target = 0.187664 restraints weight = 44725.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.188695 restraints weight = 29256.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.189430 restraints weight = 20485.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.189879 restraints weight = 14985.546| |-----------------------------------------------------------------------------| r_work (final): 0.4311 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6290 moved from start: 0.4479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 44190 Z= 0.161 Angle : 0.695 14.007 59626 Z= 0.361 Chirality : 0.046 0.200 6732 Planarity : 0.005 0.086 7614 Dihedral : 6.326 53.396 6132 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 14.19 Ramachandran Plot: Outliers : 0.17 % Allowed : 3.70 % Favored : 96.13 % Rotamer: Outliers : 6.24 % Allowed : 19.80 % Favored : 73.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.11), residues: 5432 helix: -0.24 (0.11), residues: 1952 sheet: -2.04 (0.13), residues: 1250 loop : -1.28 (0.13), residues: 2230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG J 26 TYR 0.023 0.002 TYR H 138 PHE 0.024 0.002 PHE F 97 TRP 0.017 0.002 TRP L 55 HIS 0.010 0.001 HIS V 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.16 (44174) covalent geometry : angle 0.69449 / 0.36 (59622) SS BOND : bond 0.00280 / 0.14 ( 2) SS BOND : angle 1.43897 / 0.85 ( 4) hydrogen bonds : bond 0.04320 / 2.87 ( 1202) hydrogen bonds : angle 4.62548 / 3.25 ( 3606) Misc. bond : bond 0.00356 / 0.19 ( 14) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1661 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 288 poor density : 1373 time to evaluate : 1.362 Fit side-chains TARDY: cannot create tardy model for: "ILE A 235 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU E 236 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU M 205 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE O 235 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU S 236 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU a 205 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 76 ILE cc_start: 0.7313 (OUTLIER) cc_final: 0.6043 (mp) REVERT: B 96 TYR cc_start: 0.6738 (t80) cc_final: 0.6429 (t80) REVERT: B 102 GLU cc_start: 0.6597 (OUTLIER) cc_final: 0.6333 (pm20) REVERT: B 217 PHE cc_start: 0.5208 (t80) cc_final: 0.4928 (t80) REVERT: C 12 PHE cc_start: 0.7452 (OUTLIER) cc_final: 0.7132 (m-80) REVERT: C 119 GLN cc_start: 0.6076 (tp-100) cc_final: 0.5719 (tp-100) REVERT: C 159 TRP cc_start: 0.6186 (m100) cc_final: 0.5960 (m100) REVERT: D 94 HIS cc_start: 0.8036 (t-90) cc_final: 0.7789 (t-90) REVERT: D 153 TYR cc_start: 0.7639 (p90) cc_final: 0.7427 (p90) REVERT: E 86 LYS cc_start: 0.7320 (ttpt) cc_final: 0.6874 (mtpt) REVERT: F 87 PHE cc_start: 0.7133 (t80) cc_final: 0.6715 (t80) REVERT: H 112 TYR cc_start: 0.6380 (m-80) cc_final: 0.6060 (m-80) REVERT: I 84 LYS cc_start: 0.6715 (ptmt) cc_final: 0.6484 (ptmt) REVERT: J 93 LEU cc_start: 0.7903 (tp) cc_final: 0.7681 (tp) REVERT: J 96 GLU cc_start: 0.5914 (pt0) cc_final: 0.5700 (pt0) REVERT: L 42 LEU cc_start: 0.7570 (mt) cc_final: 0.7356 (mt) REVERT: L 55 TRP cc_start: 0.7154 (m100) cc_final: 0.6823 (m100) REVERT: L 74 ILE cc_start: 0.7286 (OUTLIER) cc_final: 0.6889 (tt) REVERT: L 88 TYR cc_start: 0.6019 (t80) cc_final: 0.5712 (t80) REVERT: L 89 GLN cc_start: 0.7525 (OUTLIER) cc_final: 0.7042 (tm-30) REVERT: L 143 TYR cc_start: 0.6857 (t80) cc_final: 0.6576 (t80) REVERT: M 28 ARG cc_start: 0.5824 (ptt180) cc_final: 0.4880 (ptm160) REVERT: M 168 LEU cc_start: 0.5027 (mp) cc_final: 0.4777 (tp) REVERT: N 76 LEU cc_start: 0.6275 (OUTLIER) cc_final: 0.5854 (pp) REVERT: O 76 ILE cc_start: 0.7289 (OUTLIER) cc_final: 0.6084 (mp) REVERT: O 138 MET cc_start: 0.5999 (OUTLIER) cc_final: 0.5690 (mtt) REVERT: P 96 TYR cc_start: 0.6728 (t80) cc_final: 0.6457 (t80) REVERT: P 102 GLU cc_start: 0.6545 (OUTLIER) cc_final: 0.6303 (pm20) REVERT: P 217 PHE cc_start: 0.5218 (t80) cc_final: 0.4933 (t80) REVERT: Q 12 PHE cc_start: 0.7445 (OUTLIER) cc_final: 0.7145 (m-80) REVERT: Q 119 GLN cc_start: 0.6081 (tp-100) cc_final: 0.5726 (tp-100) REVERT: Q 159 TRP cc_start: 0.6211 (m100) cc_final: 0.5999 (m100) REVERT: R 94 HIS cc_start: 0.7998 (t-90) cc_final: 0.7696 (t-90) REVERT: S 86 LYS cc_start: 0.7308 (ttpt) cc_final: 0.6870 (mtpt) REVERT: T 16 GLN cc_start: 0.4870 (OUTLIER) cc_final: 0.3871 (mp10) REVERT: T 18 ARG cc_start: 0.5657 (mpp-170) cc_final: 0.4949 (mpt90) REVERT: T 87 PHE cc_start: 0.7150 (t80) cc_final: 0.6755 (t80) REVERT: V 112 TYR cc_start: 0.6364 (m-80) cc_final: 0.6062 (m-80) REVERT: W 84 LYS cc_start: 0.6610 (pttt) cc_final: 0.6390 (ptmt) REVERT: W 186 LEU cc_start: 0.4811 (OUTLIER) cc_final: 0.4525 (mt) REVERT: Z 42 LEU cc_start: 0.7572 (mt) cc_final: 0.7360 (mt) REVERT: Z 55 TRP cc_start: 0.7195 (m100) cc_final: 0.6846 (m100) REVERT: Z 74 ILE cc_start: 0.7280 (OUTLIER) cc_final: 0.6901 (tt) REVERT: Z 89 GLN cc_start: 0.7521 (OUTLIER) cc_final: 0.7114 (tm-30) REVERT: Z 143 TYR cc_start: 0.6848 (t80) cc_final: 0.6549 (t80) REVERT: a 71 ARG cc_start: 0.6886 (OUTLIER) cc_final: 0.6648 (mtp180) REVERT: a 168 LEU cc_start: 0.5085 (mp) cc_final: 0.4784 (tp) REVERT: a 173 ARG cc_start: 0.5340 (tpp-160) cc_final: 0.4846 (mtp85) REVERT: b 76 LEU cc_start: 0.6275 (OUTLIER) cc_final: 0.5844 (pp) outliers start: 288 outliers final: 179 residues processed: 1531 average time/residue: 0.2690 time to fit residues: 660.4320 Evaluate side-chains 1484 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 195 poor density : 1289 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 135 ILE Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 133 CYS Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain J residue 6 ASN Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 192 ASP Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 73 TYR Chi-restraints excluded: chain K residue 119 ASP Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 52 CYS Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 112 ILE Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 199 ILE Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 138 MET Chi-restraints excluded: chain O residue 159 TYR Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 207 SER Chi-restraints excluded: chain O residue 235 ILE Chi-restraints excluded: chain P residue 47 THR Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 70 HIS Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 133 LEU Chi-restraints excluded: chain P residue 135 ILE Chi-restraints excluded: chain P residue 212 CYS Chi-restraints excluded: chain Q residue 12 PHE Chi-restraints excluded: chain Q residue 28 ILE Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 100 GLN Chi-restraints excluded: chain Q residue 133 SER Chi-restraints excluded: chain Q residue 203 VAL Chi-restraints excluded: chain Q residue 224 VAL Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 141 THR Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 184 ASP Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 114 GLN Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 161 THR Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 179 SER Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 16 GLN Chi-restraints excluded: chain T residue 20 HIS Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 47 VAL Chi-restraints excluded: chain T residue 114 SER Chi-restraints excluded: chain U residue 32 ASN Chi-restraints excluded: chain U residue 70 ASP Chi-restraints excluded: chain U residue 90 ILE Chi-restraints excluded: chain U residue 133 CYS Chi-restraints excluded: chain V residue 6 VAL Chi-restraints excluded: chain V residue 8 PHE Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 94 LEU Chi-restraints excluded: chain V residue 121 VAL Chi-restraints excluded: chain V residue 169 SER Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 32 SER Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 58 LEU Chi-restraints excluded: chain W residue 81 ARG Chi-restraints excluded: chain W residue 125 VAL Chi-restraints excluded: chain W residue 186 LEU Chi-restraints excluded: chain X residue 6 ASN Chi-restraints excluded: chain X residue 90 VAL Chi-restraints excluded: chain X residue 121 CYS Chi-restraints excluded: chain X residue 192 ASP Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 26 VAL Chi-restraints excluded: chain Y residue 73 TYR Chi-restraints excluded: chain Y residue 119 ASP Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 74 ILE Chi-restraints excluded: chain Z residue 87 VAL Chi-restraints excluded: chain Z residue 89 GLN Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain Z residue 125 THR Chi-restraints excluded: chain Z residue 138 VAL Chi-restraints excluded: chain a residue 29 LEU Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain a residue 67 ILE Chi-restraints excluded: chain a residue 71 ARG Chi-restraints excluded: chain a residue 72 LEU Chi-restraints excluded: chain a residue 175 VAL Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 112 ILE Chi-restraints excluded: chain b residue 130 VAL Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 159 VAL Chi-restraints excluded: chain b residue 169 VAL Chi-restraints excluded: chain b residue 199 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 171 optimal weight: 7.9990 chunk 459 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 3 optimal weight: 7.9990 chunk 262 optimal weight: 0.9980 chunk 441 optimal weight: 4.9990 chunk 397 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 440 optimal weight: 5.9990 chunk 165 optimal weight: 4.9990 chunk 450 optimal weight: 7.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 ASN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 GLN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 HIS ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 53 GLN H 62 GLN ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 87 ASN ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 36 HIS ** N 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 33 ASN ** P 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 168 ASN R 85 ASN ** R 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 224 GLN S 225 ASN ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 7 GLN ** V 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 53 GLN V 62 GLN ** V 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 36 HIS ** b 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.194491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.189553 restraints weight = 72103.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.190828 restraints weight = 45236.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4262 r_free = 0.4262 target = 0.191669 restraints weight = 29995.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.192226 restraints weight = 21301.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.192629 restraints weight = 15933.659| |-----------------------------------------------------------------------------| r_work (final): 0.4268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6342 moved from start: 0.4710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 44190 Z= 0.177 Angle : 0.698 13.986 59626 Z= 0.363 Chirality : 0.046 0.270 6732 Planarity : 0.007 0.187 7614 Dihedral : 6.331 51.977 6132 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.09 % Favored : 95.78 % Rotamer: Outliers : 6.31 % Allowed : 21.38 % Favored : 72.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.70 (0.11), residues: 5432 helix: -0.20 (0.11), residues: 1962 sheet: -2.02 (0.14), residues: 1196 loop : -1.27 (0.13), residues: 2274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG N 186 TYR 0.025 0.002 TYR I 111 PHE 0.033 0.002 PHE Z 54 TRP 0.020 0.002 TRP X 153 HIS 0.010 0.001 HIS V 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.18 (44174) covalent geometry : angle 0.69841 / 0.36 (59622) SS BOND : bond 0.00260 / 0.13 ( 2) SS BOND : angle 1.23014 / 0.69 ( 4) hydrogen bonds : bond 0.04319 / 2.87 ( 1202) hydrogen bonds : angle 4.55644 / 3.19 ( 3606) Misc. bond : bond 0.00434 / 0.21 ( 14) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1639 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 291 poor density : 1348 time to evaluate : 1.584 Fit side-chains TARDY: cannot create tardy model for: "ILE A 235 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU E 236 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU M 205 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE O 235 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU S 236 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU a 205 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 ARG cc_start: 0.7275 (ttm170) cc_final: 0.7014 (ttm170) REVERT: B 96 TYR cc_start: 0.6826 (t80) cc_final: 0.6566 (t80) REVERT: B 102 GLU cc_start: 0.6627 (OUTLIER) cc_final: 0.6321 (pm20) REVERT: B 217 PHE cc_start: 0.5196 (t80) cc_final: 0.4903 (t80) REVERT: C 6 ASP cc_start: 0.5723 (t0) cc_final: 0.5300 (t0) REVERT: C 12 PHE cc_start: 0.7584 (OUTLIER) cc_final: 0.7227 (m-80) REVERT: C 119 GLN cc_start: 0.6195 (tp-100) cc_final: 0.5713 (tp-100) REVERT: D 153 TYR cc_start: 0.7682 (p90) cc_final: 0.7345 (p90) REVERT: E 86 LYS cc_start: 0.7450 (ttpt) cc_final: 0.6878 (mtpt) REVERT: E 91 LYS cc_start: 0.7754 (tmtt) cc_final: 0.7447 (tttm) REVERT: F 87 PHE cc_start: 0.7145 (t80) cc_final: 0.6920 (t80) REVERT: G 165 ILE cc_start: 0.8629 (pp) cc_final: 0.8344 (pp) REVERT: G 167 LYS cc_start: 0.6641 (OUTLIER) cc_final: 0.6299 (pttt) REVERT: G 197 ILE cc_start: 0.5958 (OUTLIER) cc_final: 0.5713 (mm) REVERT: I 186 LEU cc_start: 0.4918 (OUTLIER) cc_final: 0.4029 (mt) REVERT: J 93 LEU cc_start: 0.8091 (tp) cc_final: 0.7657 (tt) REVERT: L 74 ILE cc_start: 0.7326 (OUTLIER) cc_final: 0.6996 (tt) REVERT: L 89 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.7092 (tm-30) REVERT: M 28 ARG cc_start: 0.5783 (ptt180) cc_final: 0.4891 (ptm160) REVERT: M 148 LEU cc_start: 0.5082 (tt) cc_final: 0.4119 (tp) REVERT: M 168 LEU cc_start: 0.5490 (mp) cc_final: 0.4829 (tp) REVERT: N 38 ASN cc_start: 0.6005 (t0) cc_final: 0.5658 (t0) REVERT: N 76 LEU cc_start: 0.6290 (OUTLIER) cc_final: 0.5906 (pp) REVERT: N 90 SER cc_start: 0.8046 (OUTLIER) cc_final: 0.7785 (m) REVERT: P 96 TYR cc_start: 0.6812 (t80) cc_final: 0.6570 (t80) REVERT: P 102 GLU cc_start: 0.6647 (OUTLIER) cc_final: 0.6347 (pm20) REVERT: P 217 PHE cc_start: 0.5199 (t80) cc_final: 0.4901 (t80) REVERT: Q 6 ASP cc_start: 0.5721 (t0) cc_final: 0.5300 (t0) REVERT: Q 12 PHE cc_start: 0.7578 (OUTLIER) cc_final: 0.7226 (m-80) REVERT: S 91 LYS cc_start: 0.7754 (tmtt) cc_final: 0.7441 (tttm) REVERT: T 18 ARG cc_start: 0.5797 (mpp-170) cc_final: 0.5074 (mpt90) REVERT: T 90 GLN cc_start: 0.5512 (tp40) cc_final: 0.5298 (tp40) REVERT: U 165 ILE cc_start: 0.8598 (pp) cc_final: 0.8326 (pp) REVERT: U 167 LYS cc_start: 0.6626 (OUTLIER) cc_final: 0.6204 (pttt) REVERT: W 30 ASN cc_start: 0.7439 (t0) cc_final: 0.7183 (t0) REVERT: W 186 LEU cc_start: 0.4918 (OUTLIER) cc_final: 0.4650 (mt) REVERT: Z 74 ILE cc_start: 0.7357 (OUTLIER) cc_final: 0.7026 (tt) REVERT: Z 89 GLN cc_start: 0.7578 (OUTLIER) cc_final: 0.7074 (tm-30) REVERT: a 28 ARG cc_start: 0.5820 (ptt180) cc_final: 0.4908 (ptm160) REVERT: a 71 ARG cc_start: 0.6906 (OUTLIER) cc_final: 0.6694 (mtp180) REVERT: a 173 ARG cc_start: 0.5499 (tpp-160) cc_final: 0.4931 (mtp85) REVERT: b 76 LEU cc_start: 0.6287 (OUTLIER) cc_final: 0.5905 (pp) REVERT: b 90 SER cc_start: 0.8030 (OUTLIER) cc_final: 0.7792 (m) outliers start: 291 outliers final: 202 residues processed: 1515 average time/residue: 0.2606 time to fit residues: 637.5821 Evaluate side-chains 1495 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 220 poor density : 1275 time to evaluate : 1.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 64 VAL Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 133 SER Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 141 THR Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 98 ASN Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 179 SER Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 133 CYS Chi-restraints excluded: chain G residue 167 LYS Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 81 ARG Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain J residue 90 VAL Chi-restraints excluded: chain J residue 121 CYS Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 192 ASP Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 73 TYR Chi-restraints excluded: chain K residue 119 ASP Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain M residue 12 ILE Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 72 LEU Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain N residue 42 ILE Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 90 SER Chi-restraints excluded: chain N residue 112 ILE Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 84 THR Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 159 TYR Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 207 SER Chi-restraints excluded: chain O residue 235 ILE Chi-restraints excluded: chain P residue 47 THR Chi-restraints excluded: chain P residue 64 VAL Chi-restraints excluded: chain P residue 70 HIS Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain P residue 133 LEU Chi-restraints excluded: chain P residue 212 CYS Chi-restraints excluded: chain Q residue 12 PHE Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 100 GLN Chi-restraints excluded: chain Q residue 133 SER Chi-restraints excluded: chain Q residue 203 VAL Chi-restraints excluded: chain Q residue 224 VAL Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 141 THR Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 98 ASN Chi-restraints excluded: chain S residue 114 GLN Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 161 THR Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 179 SER Chi-restraints excluded: chain S residue 191 LEU Chi-restraints excluded: chain S residue 215 ILE Chi-restraints excluded: chain S residue 220 VAL Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 20 HIS Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 47 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 114 SER Chi-restraints excluded: chain U residue 32 ASN Chi-restraints excluded: chain U residue 50 GLU Chi-restraints excluded: chain U residue 70 ASP Chi-restraints excluded: chain U residue 90 ILE Chi-restraints excluded: chain U residue 133 CYS Chi-restraints excluded: chain U residue 167 LYS Chi-restraints excluded: chain U residue 199 ILE Chi-restraints excluded: chain V residue 6 VAL Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 94 LEU Chi-restraints excluded: chain V residue 103 TRP Chi-restraints excluded: chain V residue 121 VAL Chi-restraints excluded: chain V residue 169 SER Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 32 SER Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 81 ARG Chi-restraints excluded: chain W residue 125 VAL Chi-restraints excluded: chain W residue 186 LEU Chi-restraints excluded: chain X residue 90 VAL Chi-restraints excluded: chain X residue 121 CYS Chi-restraints excluded: chain X residue 174 VAL Chi-restraints excluded: chain X residue 192 ASP Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 53 THR Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 73 TYR Chi-restraints excluded: chain Y residue 119 ASP Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 74 ILE Chi-restraints excluded: chain Z residue 87 VAL Chi-restraints excluded: chain Z residue 89 GLN Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain Z residue 125 THR Chi-restraints excluded: chain Z residue 138 VAL Chi-restraints excluded: chain a residue 12 ILE Chi-restraints excluded: chain a residue 22 ILE Chi-restraints excluded: chain a residue 29 LEU Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain a residue 67 ILE Chi-restraints excluded: chain a residue 71 ARG Chi-restraints excluded: chain a residue 72 LEU Chi-restraints excluded: chain a residue 175 VAL Chi-restraints excluded: chain b residue 42 ILE Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 90 SER Chi-restraints excluded: chain b residue 112 ILE Chi-restraints excluded: chain b residue 130 VAL Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 159 VAL Chi-restraints excluded: chain b residue 169 VAL Chi-restraints excluded: chain b residue 189 ILE Chi-restraints excluded: chain b residue 191 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 192 optimal weight: 9.9990 chunk 447 optimal weight: 6.9990 chunk 171 optimal weight: 8.9990 chunk 318 optimal weight: 6.9990 chunk 276 optimal weight: 8.9990 chunk 499 optimal weight: 2.9990 chunk 505 optimal weight: 9.9990 chunk 252 optimal weight: 20.0000 chunk 73 optimal weight: 10.0000 chunk 130 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 ASN F 90 GLN F 117 GLN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 HIS ** N 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 33 ASN ** P 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 117 GLN ** V 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 85 GLN ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 77 HIS ** b 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.184038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.178303 restraints weight = 73776.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.179780 restraints weight = 44086.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.180781 restraints weight = 28782.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.181491 restraints weight = 19984.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.181944 restraints weight = 14490.094| |-----------------------------------------------------------------------------| r_work (final): 0.4187 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6489 moved from start: 0.4819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.082 44190 Z= 0.302 Angle : 0.862 13.987 59626 Z= 0.446 Chirality : 0.052 0.276 6732 Planarity : 0.007 0.176 7614 Dihedral : 6.956 55.676 6132 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 19.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.17 % Favored : 93.70 % Rotamer: Outliers : 7.42 % Allowed : 22.20 % Favored : 70.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.18 (0.11), residues: 5432 helix: -0.67 (0.11), residues: 1946 sheet: -2.24 (0.13), residues: 1272 loop : -1.45 (0.13), residues: 2214 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG b 186 TYR 0.041 0.003 TYR H 61 PHE 0.029 0.003 PHE J 116 TRP 0.030 0.003 TRP X 153 HIS 0.013 0.002 HIS V 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00680 / 0.30 (44174) covalent geometry : angle 0.86215 / 0.45 (59622) SS BOND : bond 0.00009 / 0.00 ( 2) SS BOND : angle 0.97448 / 0.57 ( 4) hydrogen bonds : bond 0.05151 / 3.40 ( 1202) hydrogen bonds : angle 5.00790 / 3.49 ( 3606) Misc. bond : bond 0.00378 / 0.19 ( 14) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1646 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 342 poor density : 1304 time to evaluate : 1.107 Fit side-chains TARDY: cannot create tardy model for: "ILE A 235 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU E 236 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE O 235 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU S 236 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 83 ARG cc_start: 0.6920 (mtt90) cc_final: 0.6450 (ttm110) REVERT: B 96 TYR cc_start: 0.6875 (t80) cc_final: 0.6625 (t80) REVERT: B 102 GLU cc_start: 0.6681 (OUTLIER) cc_final: 0.6362 (pm20) REVERT: B 217 PHE cc_start: 0.5497 (t80) cc_final: 0.5294 (t80) REVERT: C 12 PHE cc_start: 0.7751 (OUTLIER) cc_final: 0.7359 (m-80) REVERT: C 25 MET cc_start: 0.6647 (mmp) cc_final: 0.6307 (mmp) REVERT: D 153 TYR cc_start: 0.7744 (p90) cc_final: 0.7440 (p90) REVERT: E 86 LYS cc_start: 0.7634 (ttpt) cc_final: 0.7103 (mtpt) REVERT: E 91 LYS cc_start: 0.7891 (tmtt) cc_final: 0.7568 (tttm) REVERT: G 167 LYS cc_start: 0.6737 (OUTLIER) cc_final: 0.6453 (pttt) REVERT: I 81 ARG cc_start: 0.6239 (OUTLIER) cc_final: 0.5806 (ttt-90) REVERT: I 186 LEU cc_start: 0.5194 (OUTLIER) cc_final: 0.4106 (mt) REVERT: I 203 ARG cc_start: 0.5397 (mmt90) cc_final: 0.4395 (ptm-80) REVERT: J 93 LEU cc_start: 0.7823 (tp) cc_final: 0.7587 (tp) REVERT: J 145 MET cc_start: 0.6465 (OUTLIER) cc_final: 0.6115 (mtp) REVERT: L 89 GLN cc_start: 0.7550 (OUTLIER) cc_final: 0.7096 (tm-30) REVERT: L 143 TYR cc_start: 0.7449 (t80) cc_final: 0.6886 (t80) REVERT: M 18 GLU cc_start: 0.5560 (pt0) cc_final: 0.5251 (pt0) REVERT: M 28 ARG cc_start: 0.6090 (ptt180) cc_final: 0.4980 (ptm160) REVERT: N 76 LEU cc_start: 0.6443 (OUTLIER) cc_final: 0.6065 (pp) REVERT: N 112 ILE cc_start: 0.6306 (OUTLIER) cc_final: 0.6059 (mp) REVERT: P 83 ARG cc_start: 0.6953 (mtt90) cc_final: 0.6461 (ttm110) REVERT: P 96 TYR cc_start: 0.6860 (t80) cc_final: 0.6632 (t80) REVERT: P 102 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.6380 (pm20) REVERT: Q 12 PHE cc_start: 0.7730 (OUTLIER) cc_final: 0.7346 (m-80) REVERT: Q 25 MET cc_start: 0.6579 (mmp) cc_final: 0.6247 (mmp) REVERT: R 153 TYR cc_start: 0.7621 (p90) cc_final: 0.7322 (p90) REVERT: S 91 LYS cc_start: 0.7886 (tmtt) cc_final: 0.7569 (tttm) REVERT: T 18 ARG cc_start: 0.5776 (mpp-170) cc_final: 0.5101 (mpt90) REVERT: U 167 LYS cc_start: 0.6766 (OUTLIER) cc_final: 0.6453 (pptt) REVERT: W 81 ARG cc_start: 0.6383 (OUTLIER) cc_final: 0.5749 (ttt-90) REVERT: W 203 ARG cc_start: 0.5406 (mmt90) cc_final: 0.4369 (ptm-80) REVERT: Z 89 GLN cc_start: 0.7512 (OUTLIER) cc_final: 0.7076 (tm-30) REVERT: Z 143 TYR cc_start: 0.7595 (t80) cc_final: 0.4560 (t80) REVERT: a 28 ARG cc_start: 0.6002 (ptt180) cc_final: 0.4975 (ptm160) REVERT: a 71 ARG cc_start: 0.7021 (OUTLIER) cc_final: 0.6611 (mtp180) REVERT: a 149 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7443 (tp) REVERT: a 173 ARG cc_start: 0.5645 (tpp-160) cc_final: 0.4802 (mtp85) REVERT: b 5 MET cc_start: 0.6132 (mmt) cc_final: 0.5771 (mmt) REVERT: b 76 LEU cc_start: 0.6433 (OUTLIER) cc_final: 0.6041 (pp) REVERT: b 112 ILE cc_start: 0.6279 (OUTLIER) cc_final: 0.6029 (mp) outliers start: 342 outliers final: 240 residues processed: 1524 average time/residue: 0.2595 time to fit residues: 640.9530 Evaluate side-chains 1514 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 258 poor density : 1256 time to evaluate : 1.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 118 GLN Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 228 TYR Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 77 LEU Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 133 CYS Chi-restraints excluded: chain G residue 135 PHE Chi-restraints excluded: chain G residue 167 LYS Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain G residue 219 LEU Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 81 ARG Chi-restraints excluded: chain I residue 94 ILE Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain J residue 41 ILE Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 121 CYS Chi-restraints excluded: chain J residue 145 MET Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 192 ASP Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 73 TYR Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 133 ASP Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 198 VAL Chi-restraints excluded: chain N residue 42 ILE Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 112 ILE Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain N residue 193 THR Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 79 VAL Chi-restraints excluded: chain O residue 84 THR Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 159 TYR Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 207 SER Chi-restraints excluded: chain O residue 235 ILE Chi-restraints excluded: chain P residue 47 THR Chi-restraints excluded: chain P residue 70 HIS Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain P residue 133 LEU Chi-restraints excluded: chain P residue 180 ASP Chi-restraints excluded: chain P residue 191 ILE Chi-restraints excluded: chain P residue 212 CYS Chi-restraints excluded: chain Q residue 12 PHE Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 100 GLN Chi-restraints excluded: chain Q residue 203 VAL Chi-restraints excluded: chain Q residue 224 VAL Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 108 THR Chi-restraints excluded: chain R residue 141 THR Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 167 SER Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 184 ASP Chi-restraints excluded: chain R residue 185 ASP Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 228 TYR Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 114 GLN Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 161 THR Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 191 LEU Chi-restraints excluded: chain S residue 205 VAL Chi-restraints excluded: chain S residue 215 ILE Chi-restraints excluded: chain S residue 220 VAL Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 47 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 77 LEU Chi-restraints excluded: chain T residue 114 SER Chi-restraints excluded: chain U residue 32 ASN Chi-restraints excluded: chain U residue 50 GLU Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 70 ASP Chi-restraints excluded: chain U residue 90 ILE Chi-restraints excluded: chain U residue 133 CYS Chi-restraints excluded: chain U residue 135 PHE Chi-restraints excluded: chain U residue 167 LYS Chi-restraints excluded: chain U residue 199 ILE Chi-restraints excluded: chain U residue 219 LEU Chi-restraints excluded: chain V residue 6 VAL Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 103 TRP Chi-restraints excluded: chain V residue 121 VAL Chi-restraints excluded: chain V residue 160 LEU Chi-restraints excluded: chain V residue 169 SER Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 25 VAL Chi-restraints excluded: chain W residue 32 SER Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 58 LEU Chi-restraints excluded: chain W residue 81 ARG Chi-restraints excluded: chain W residue 94 ILE Chi-restraints excluded: chain W residue 110 LEU Chi-restraints excluded: chain W residue 125 VAL Chi-restraints excluded: chain W residue 186 LEU Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 121 CYS Chi-restraints excluded: chain X residue 152 LEU Chi-restraints excluded: chain X residue 174 VAL Chi-restraints excluded: chain X residue 192 ASP Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 26 VAL Chi-restraints excluded: chain Y residue 53 THR Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 73 TYR Chi-restraints excluded: chain Y residue 121 LEU Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 74 ILE Chi-restraints excluded: chain Z residue 87 VAL Chi-restraints excluded: chain Z residue 89 GLN Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain Z residue 125 THR Chi-restraints excluded: chain Z residue 138 VAL Chi-restraints excluded: chain a residue 22 ILE Chi-restraints excluded: chain a residue 29 LEU Chi-restraints excluded: chain a residue 35 ILE Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain a residue 67 ILE Chi-restraints excluded: chain a residue 71 ARG Chi-restraints excluded: chain a residue 133 ASP Chi-restraints excluded: chain a residue 149 LEU Chi-restraints excluded: chain a residue 175 VAL Chi-restraints excluded: chain a residue 198 VAL Chi-restraints excluded: chain b residue 42 ILE Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 112 ILE Chi-restraints excluded: chain b residue 130 VAL Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 159 VAL Chi-restraints excluded: chain b residue 169 VAL Chi-restraints excluded: chain b residue 189 ILE Chi-restraints excluded: chain b residue 191 THR Chi-restraints excluded: chain b residue 193 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 481 optimal weight: 0.0770 chunk 459 optimal weight: 5.9990 chunk 44 optimal weight: 20.0000 chunk 160 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 480 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 chunk 63 optimal weight: 9.9990 chunk 122 optimal weight: 3.9990 chunk 420 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 overall best weight: 4.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** G 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 187 HIS ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 87 ASN ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 80 ASN ** N 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 85 GLN X 187 HIS ** Z 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 80 ASN ** b 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.190142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.184954 restraints weight = 72392.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.186263 restraints weight = 46586.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.187179 restraints weight = 30865.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.187790 restraints weight = 21813.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.188177 restraints weight = 16200.067| |-----------------------------------------------------------------------------| r_work (final): 0.4216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 moved from start: 0.5025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 44190 Z= 0.223 Angle : 0.772 14.154 59626 Z= 0.399 Chirality : 0.048 0.249 6732 Planarity : 0.006 0.132 7614 Dihedral : 6.743 59.874 6130 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 18.05 Ramachandran Plot: Outliers : 0.13 % Allowed : 5.36 % Favored : 94.51 % Rotamer: Outliers : 6.85 % Allowed : 23.63 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.11), residues: 5432 helix: -0.58 (0.11), residues: 1950 sheet: -2.26 (0.13), residues: 1270 loop : -1.51 (0.13), residues: 2212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG b 186 TYR 0.033 0.002 TYR V 90 PHE 0.027 0.002 PHE b 16 TRP 0.028 0.003 TRP J 153 HIS 0.011 0.002 HIS Q 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.22 (44174) covalent geometry : angle 0.77137 / 0.40 (59622) SS BOND : bond 0.00943 / 0.47 ( 2) SS BOND : angle 2.32983 / 1.48 ( 4) hydrogen bonds : bond 0.04691 / 3.09 ( 1202) hydrogen bonds : angle 4.84690 / 3.38 ( 3606) Misc. bond : bond 0.00366 / 0.19 ( 14) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1614 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 316 poor density : 1298 time to evaluate : 1.741 Fit side-chains TARDY: cannot create tardy model for: "ILE A 235 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU E 236 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU M 205 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE O 235 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU S 236 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU a 205 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: B 83 ARG cc_start: 0.6832 (mtt90) cc_final: 0.6462 (ttm110) REVERT: B 96 TYR cc_start: 0.6879 (t80) cc_final: 0.6460 (t80) REVERT: B 102 GLU cc_start: 0.6730 (OUTLIER) cc_final: 0.6371 (pm20) REVERT: C 12 PHE cc_start: 0.7621 (OUTLIER) cc_final: 0.7237 (m-80) REVERT: C 25 MET cc_start: 0.6563 (mmp) cc_final: 0.6338 (mmp) REVERT: D 153 TYR cc_start: 0.7728 (p90) cc_final: 0.7409 (p90) REVERT: E 86 LYS cc_start: 0.7584 (ttpt) cc_final: 0.7060 (mtpt) REVERT: F 125 ARG cc_start: 0.5767 (mmt180) cc_final: 0.5394 (mmt90) REVERT: F 157 ARG cc_start: 0.4855 (OUTLIER) cc_final: 0.3887 (mtm-85) REVERT: G 167 LYS cc_start: 0.6677 (OUTLIER) cc_final: 0.6387 (pptt) REVERT: I 81 ARG cc_start: 0.6203 (OUTLIER) cc_final: 0.5640 (ttt-90) REVERT: I 186 LEU cc_start: 0.5124 (OUTLIER) cc_final: 0.4423 (mt) REVERT: I 203 ARG cc_start: 0.5037 (mmt90) cc_final: 0.4235 (ptm-80) REVERT: J 26 ARG cc_start: 0.7059 (tmt-80) cc_final: 0.6649 (tmt-80) REVERT: J 145 MET cc_start: 0.6612 (OUTLIER) cc_final: 0.6200 (mtt) REVERT: L 88 TYR cc_start: 0.6281 (t80) cc_final: 0.5996 (t80) REVERT: L 89 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.6970 (tm-30) REVERT: M 28 ARG cc_start: 0.5948 (ptt180) cc_final: 0.4865 (ptm160) REVERT: M 66 LYS cc_start: 0.8396 (mtmm) cc_final: 0.8116 (mtmm) REVERT: N 76 LEU cc_start: 0.6491 (OUTLIER) cc_final: 0.6203 (pp) REVERT: N 77 LEU cc_start: 0.7063 (mt) cc_final: 0.6750 (mt) REVERT: N 112 ILE cc_start: 0.6168 (OUTLIER) cc_final: 0.5877 (mp) REVERT: N 186 ARG cc_start: 0.4521 (OUTLIER) cc_final: 0.3495 (tpm170) REVERT: P 83 ARG cc_start: 0.6856 (mtt90) cc_final: 0.6470 (ttm110) REVERT: P 96 TYR cc_start: 0.6898 (t80) cc_final: 0.6481 (t80) REVERT: P 102 GLU cc_start: 0.6712 (OUTLIER) cc_final: 0.6352 (pm20) REVERT: Q 12 PHE cc_start: 0.7597 (OUTLIER) cc_final: 0.7215 (m-80) REVERT: Q 48 GLU cc_start: 0.6129 (OUTLIER) cc_final: 0.5765 (tp30) REVERT: R 153 TYR cc_start: 0.7701 (p90) cc_final: 0.7339 (p90) REVERT: T 18 ARG cc_start: 0.5725 (mpp-170) cc_final: 0.5034 (mpt90) REVERT: T 125 ARG cc_start: 0.5806 (mmt180) cc_final: 0.5444 (mmt90) REVERT: T 157 ARG cc_start: 0.4840 (OUTLIER) cc_final: 0.3885 (mtm-85) REVERT: U 167 LYS cc_start: 0.6697 (OUTLIER) cc_final: 0.6374 (pttt) REVERT: W 30 ASN cc_start: 0.7661 (t0) cc_final: 0.7443 (t0) REVERT: W 203 ARG cc_start: 0.5042 (mmt90) cc_final: 0.4242 (ptm-80) REVERT: X 26 ARG cc_start: 0.7089 (tmt-80) cc_final: 0.6633 (tmt-80) REVERT: X 145 MET cc_start: 0.6617 (OUTLIER) cc_final: 0.6203 (mtt) REVERT: Z 89 GLN cc_start: 0.7509 (OUTLIER) cc_final: 0.7069 (tm-30) REVERT: Z 143 TYR cc_start: 0.7499 (t80) cc_final: 0.4417 (t80) REVERT: a 28 ARG cc_start: 0.5993 (ptt180) cc_final: 0.4947 (ptm160) REVERT: a 66 LYS cc_start: 0.8448 (mtmm) cc_final: 0.8123 (mtmm) REVERT: a 71 ARG cc_start: 0.6948 (OUTLIER) cc_final: 0.6649 (mtp180) REVERT: a 168 LEU cc_start: 0.5176 (mp) cc_final: 0.4575 (tp) REVERT: a 173 ARG cc_start: 0.5676 (tpp-160) cc_final: 0.4845 (mtp85) REVERT: b 5 MET cc_start: 0.6121 (mmt) cc_final: 0.5774 (mmt) REVERT: b 76 LEU cc_start: 0.6398 (OUTLIER) cc_final: 0.6095 (pp) REVERT: b 77 LEU cc_start: 0.7039 (mt) cc_final: 0.6739 (mt) REVERT: b 112 ILE cc_start: 0.6172 (OUTLIER) cc_final: 0.5835 (mp) REVERT: b 186 ARG cc_start: 0.4548 (OUTLIER) cc_final: 0.3438 (tpm170) outliers start: 316 outliers final: 237 residues processed: 1500 average time/residue: 0.2624 time to fit residues: 637.7049 Evaluate side-chains 1503 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 259 poor density : 1244 time to evaluate : 1.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain F residue 157 ARG Chi-restraints excluded: chain F residue 174 ARG Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 133 CYS Chi-restraints excluded: chain G residue 167 LYS Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 25 VAL Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 81 ARG Chi-restraints excluded: chain I residue 120 ASP Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain J residue 41 ILE Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 70 LEU Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 121 CYS Chi-restraints excluded: chain J residue 145 MET Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 192 ASP Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 73 TYR Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 45 MET Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 89 GLN Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain N residue 42 ILE Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 88 ILE Chi-restraints excluded: chain N residue 112 ILE Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 186 ARG Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain N residue 193 THR Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 84 THR Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 159 TYR Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 196 GLU Chi-restraints excluded: chain O residue 207 SER Chi-restraints excluded: chain O residue 217 VAL Chi-restraints excluded: chain O residue 235 ILE Chi-restraints excluded: chain P residue 47 THR Chi-restraints excluded: chain P residue 70 HIS Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain P residue 133 LEU Chi-restraints excluded: chain P residue 171 THR Chi-restraints excluded: chain P residue 212 CYS Chi-restraints excluded: chain Q residue 12 PHE Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 48 GLU Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 100 GLN Chi-restraints excluded: chain Q residue 203 VAL Chi-restraints excluded: chain Q residue 224 VAL Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 141 THR Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 184 ASP Chi-restraints excluded: chain R residue 185 ASP Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 114 GLN Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 161 THR Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 191 LEU Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 215 ILE Chi-restraints excluded: chain S residue 220 VAL Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 47 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 114 SER Chi-restraints excluded: chain T residue 157 ARG Chi-restraints excluded: chain T residue 174 ARG Chi-restraints excluded: chain U residue 32 ASN Chi-restraints excluded: chain U residue 35 THR Chi-restraints excluded: chain U residue 50 GLU Chi-restraints excluded: chain U residue 70 ASP Chi-restraints excluded: chain U residue 90 ILE Chi-restraints excluded: chain U residue 133 CYS Chi-restraints excluded: chain U residue 167 LYS Chi-restraints excluded: chain U residue 199 ILE Chi-restraints excluded: chain V residue 6 VAL Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 98 ILE Chi-restraints excluded: chain V residue 103 TRP Chi-restraints excluded: chain V residue 121 VAL Chi-restraints excluded: chain V residue 169 SER Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 32 SER Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 58 LEU Chi-restraints excluded: chain W residue 110 LEU Chi-restraints excluded: chain W residue 120 ASP Chi-restraints excluded: chain W residue 125 VAL Chi-restraints excluded: chain W residue 169 SER Chi-restraints excluded: chain X residue 41 ILE Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 77 GLU Chi-restraints excluded: chain X residue 121 CYS Chi-restraints excluded: chain X residue 145 MET Chi-restraints excluded: chain X residue 152 LEU Chi-restraints excluded: chain X residue 174 VAL Chi-restraints excluded: chain X residue 192 ASP Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain Y residue 53 THR Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 73 TYR Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 51 ASP Chi-restraints excluded: chain Z residue 74 ILE Chi-restraints excluded: chain Z residue 87 VAL Chi-restraints excluded: chain Z residue 89 GLN Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain Z residue 125 THR Chi-restraints excluded: chain Z residue 138 VAL Chi-restraints excluded: chain a residue 11 THR Chi-restraints excluded: chain a residue 22 ILE Chi-restraints excluded: chain a residue 29 LEU Chi-restraints excluded: chain a residue 35 ILE Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain a residue 67 ILE Chi-restraints excluded: chain a residue 71 ARG Chi-restraints excluded: chain a residue 175 VAL Chi-restraints excluded: chain b residue 42 ILE Chi-restraints excluded: chain b residue 43 MET Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 88 ILE Chi-restraints excluded: chain b residue 112 ILE Chi-restraints excluded: chain b residue 130 VAL Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 159 VAL Chi-restraints excluded: chain b residue 169 VAL Chi-restraints excluded: chain b residue 186 ARG Chi-restraints excluded: chain b residue 189 ILE Chi-restraints excluded: chain b residue 191 THR Chi-restraints excluded: chain b residue 193 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 275 optimal weight: 6.9990 chunk 201 optimal weight: 8.9990 chunk 430 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 283 optimal weight: 8.9990 chunk 103 optimal weight: 10.0000 chunk 380 optimal weight: 30.0000 chunk 27 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 187 HIS ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 77 HIS M 80 ASN ** N 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 53 GLN ** W 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 187 HIS ** Y 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 77 HIS a 80 ASN ** b 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4232 r_free = 0.4232 target = 0.188725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.183509 restraints weight = 73480.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.184888 restraints weight = 45259.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.185791 restraints weight = 30343.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.186378 restraints weight = 21493.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.186807 restraints weight = 16053.063| |-----------------------------------------------------------------------------| r_work (final): 0.4212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6476 moved from start: 0.5144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 44190 Z= 0.258 Angle : 0.822 14.081 59626 Z= 0.425 Chirality : 0.051 0.272 6732 Planarity : 0.007 0.133 7614 Dihedral : 6.891 59.324 6130 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.13 % Allowed : 6.63 % Favored : 93.24 % Rotamer: Outliers : 7.26 % Allowed : 23.81 % Favored : 68.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.33 (0.11), residues: 5432 helix: -0.70 (0.11), residues: 1944 sheet: -2.38 (0.13), residues: 1250 loop : -1.61 (0.13), residues: 2238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG U 114 TYR 0.033 0.003 TYR H 61 PHE 0.030 0.003 PHE N 16 TRP 0.031 0.003 TRP J 153 HIS 0.012 0.002 HIS C 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00590 / 0.26 (44174) covalent geometry : angle 0.82170 / 0.43 (59622) SS BOND : bond 0.00135 / 0.07 ( 2) SS BOND : angle 1.74311 / 1.02 ( 4) hydrogen bonds : bond 0.04922 / 3.23 ( 1202) hydrogen bonds : angle 4.98554 / 3.48 ( 3606) Misc. bond : bond 0.00331 / 0.17 ( 14) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1608 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 335 poor density : 1273 time to evaluate : 1.658 Fit side-chains TARDY: cannot create tardy model for: "ILE A 235 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU E 236 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU M 205 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE O 235 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU S 236 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU a 205 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: B 83 ARG cc_start: 0.6945 (mtt90) cc_final: 0.6629 (ttm110) REVERT: B 102 GLU cc_start: 0.6716 (OUTLIER) cc_final: 0.6393 (pm20) REVERT: B 127 ARG cc_start: 0.6106 (ptt90) cc_final: 0.5888 (ptt90) REVERT: C 12 PHE cc_start: 0.7604 (OUTLIER) cc_final: 0.7187 (m-80) REVERT: C 25 MET cc_start: 0.6656 (mmp) cc_final: 0.6391 (mmp) REVERT: C 48 GLU cc_start: 0.6191 (OUTLIER) cc_final: 0.5789 (tp30) REVERT: D 153 TYR cc_start: 0.7746 (p90) cc_final: 0.7461 (p90) REVERT: E 86 LYS cc_start: 0.7577 (ttpt) cc_final: 0.7066 (mtpt) REVERT: E 189 MET cc_start: 0.3597 (OUTLIER) cc_final: 0.2823 (tpp) REVERT: F 125 ARG cc_start: 0.5823 (mmt180) cc_final: 0.5466 (mmt90) REVERT: F 157 ARG cc_start: 0.4972 (OUTLIER) cc_final: 0.4212 (mtm-85) REVERT: G 167 LYS cc_start: 0.6713 (OUTLIER) cc_final: 0.6392 (pttt) REVERT: I 81 ARG cc_start: 0.6097 (OUTLIER) cc_final: 0.5615 (ttt-90) REVERT: I 186 LEU cc_start: 0.5235 (OUTLIER) cc_final: 0.4631 (mt) REVERT: I 203 ARG cc_start: 0.5196 (mmt90) cc_final: 0.4139 (ptm-80) REVERT: J 145 MET cc_start: 0.6561 (OUTLIER) cc_final: 0.6164 (mtt) REVERT: K 139 THR cc_start: 0.6845 (p) cc_final: 0.6635 (m) REVERT: M 28 ARG cc_start: 0.6057 (ptt180) cc_final: 0.4951 (ptm160) REVERT: M 66 LYS cc_start: 0.8386 (mtmm) cc_final: 0.8015 (mtmm) REVERT: N 76 LEU cc_start: 0.6461 (OUTLIER) cc_final: 0.6119 (pp) REVERT: N 86 ARG cc_start: 0.7502 (mmt-90) cc_final: 0.6927 (mmm160) REVERT: N 90 SER cc_start: 0.8162 (OUTLIER) cc_final: 0.7830 (m) REVERT: N 186 ARG cc_start: 0.4583 (OUTLIER) cc_final: 0.3977 (tpm170) REVERT: P 102 GLU cc_start: 0.6704 (OUTLIER) cc_final: 0.6402 (pm20) REVERT: Q 12 PHE cc_start: 0.7590 (OUTLIER) cc_final: 0.7190 (m-80) REVERT: Q 48 GLU cc_start: 0.6184 (OUTLIER) cc_final: 0.5794 (tp30) REVERT: R 153 TYR cc_start: 0.7675 (p90) cc_final: 0.7331 (p90) REVERT: S 189 MET cc_start: 0.3590 (OUTLIER) cc_final: 0.2757 (tpp) REVERT: T 18 ARG cc_start: 0.5717 (mpp-170) cc_final: 0.5137 (mpt90) REVERT: T 125 ARG cc_start: 0.5939 (mmt180) cc_final: 0.5574 (mmt90) REVERT: T 157 ARG cc_start: 0.4954 (OUTLIER) cc_final: 0.4190 (mtm-85) REVERT: U 167 LYS cc_start: 0.6699 (OUTLIER) cc_final: 0.6350 (pttt) REVERT: W 81 ARG cc_start: 0.6303 (OUTLIER) cc_final: 0.5736 (ttt-90) REVERT: W 203 ARG cc_start: 0.5044 (mmt90) cc_final: 0.4151 (ptm-80) REVERT: X 145 MET cc_start: 0.6577 (OUTLIER) cc_final: 0.6051 (mtt) REVERT: Z 89 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.7126 (tm-30) REVERT: a 28 ARG cc_start: 0.6042 (ptt180) cc_final: 0.4924 (ptm160) REVERT: a 71 ARG cc_start: 0.6979 (OUTLIER) cc_final: 0.6637 (mtp180) REVERT: a 173 ARG cc_start: 0.5744 (tpp-160) cc_final: 0.4897 (mtp85) REVERT: b 5 MET cc_start: 0.6129 (mmt) cc_final: 0.5793 (mmt) REVERT: b 76 LEU cc_start: 0.6432 (OUTLIER) cc_final: 0.6075 (pp) REVERT: b 86 ARG cc_start: 0.7471 (mmt-90) cc_final: 0.7163 (mmm160) REVERT: b 186 ARG cc_start: 0.4595 (OUTLIER) cc_final: 0.3989 (tpm170) outliers start: 335 outliers final: 277 residues processed: 1486 average time/residue: 0.2813 time to fit residues: 676.4876 Evaluate side-chains 1538 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 301 poor density : 1237 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 ASP Chi-restraints excluded: chain A residue 51 VAL Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 196 GLU Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain A residue 217 VAL Chi-restraints excluded: chain A residue 235 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 85 LEU Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain B residue 171 THR Chi-restraints excluded: chain B residue 180 ASP Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 80 THR Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 89 VAL Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 161 ILE Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 188 ILE Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain E residue 24 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 189 MET Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 205 VAL Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 114 SER Chi-restraints excluded: chain F residue 157 ARG Chi-restraints excluded: chain F residue 174 ARG Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 69 VAL Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 133 CYS Chi-restraints excluded: chain G residue 167 LYS Chi-restraints excluded: chain G residue 199 ILE Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 13 VAL Chi-restraints excluded: chain H residue 21 THR Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain I residue 21 THR Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 81 ARG Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 105 VAL Chi-restraints excluded: chain I residue 120 ASP Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 186 LEU Chi-restraints excluded: chain J residue 41 ILE Chi-restraints excluded: chain J residue 55 LEU Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 70 LEU Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 121 CYS Chi-restraints excluded: chain J residue 145 MET Chi-restraints excluded: chain J residue 152 LEU Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 192 ASP Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain K residue 73 TYR Chi-restraints excluded: chain K residue 121 LEU Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 121 ILE Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain L residue 138 VAL Chi-restraints excluded: chain M residue 29 LEU Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 133 ASP Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain M residue 198 VAL Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 42 ILE Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 88 ILE Chi-restraints excluded: chain N residue 90 SER Chi-restraints excluded: chain N residue 112 ILE Chi-restraints excluded: chain N residue 130 VAL Chi-restraints excluded: chain N residue 159 VAL Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 186 ARG Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain N residue 191 THR Chi-restraints excluded: chain N residue 193 THR Chi-restraints excluded: chain O residue 19 GLU Chi-restraints excluded: chain O residue 46 ASP Chi-restraints excluded: chain O residue 51 VAL Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 84 THR Chi-restraints excluded: chain O residue 112 ASP Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 159 TYR Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 196 GLU Chi-restraints excluded: chain O residue 207 SER Chi-restraints excluded: chain O residue 217 VAL Chi-restraints excluded: chain O residue 235 ILE Chi-restraints excluded: chain P residue 47 THR Chi-restraints excluded: chain P residue 70 HIS Chi-restraints excluded: chain P residue 85 LEU Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain P residue 133 LEU Chi-restraints excluded: chain P residue 171 THR Chi-restraints excluded: chain P residue 180 ASP Chi-restraints excluded: chain P residue 191 ILE Chi-restraints excluded: chain P residue 212 CYS Chi-restraints excluded: chain Q residue 12 PHE Chi-restraints excluded: chain Q residue 25 MET Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 44 LEU Chi-restraints excluded: chain Q residue 48 GLU Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 80 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 100 GLN Chi-restraints excluded: chain Q residue 155 ASN Chi-restraints excluded: chain Q residue 203 VAL Chi-restraints excluded: chain Q residue 224 VAL Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 89 VAL Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 141 THR Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 167 SER Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 184 ASP Chi-restraints excluded: chain R residue 185 ASP Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 88 LEU Chi-restraints excluded: chain S residue 114 GLN Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 139 VAL Chi-restraints excluded: chain S residue 153 LEU Chi-restraints excluded: chain S residue 161 THR Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 189 MET Chi-restraints excluded: chain S residue 191 LEU Chi-restraints excluded: chain S residue 205 VAL Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 215 ILE Chi-restraints excluded: chain S residue 220 VAL Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain T residue 10 VAL Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 47 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 114 SER Chi-restraints excluded: chain T residue 157 ARG Chi-restraints excluded: chain T residue 174 ARG Chi-restraints excluded: chain U residue 32 ASN Chi-restraints excluded: chain U residue 35 THR Chi-restraints excluded: chain U residue 50 GLU Chi-restraints excluded: chain U residue 69 VAL Chi-restraints excluded: chain U residue 70 ASP Chi-restraints excluded: chain U residue 90 ILE Chi-restraints excluded: chain U residue 133 CYS Chi-restraints excluded: chain U residue 167 LYS Chi-restraints excluded: chain U residue 199 ILE Chi-restraints excluded: chain V residue 6 VAL Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 98 ILE Chi-restraints excluded: chain V residue 103 TRP Chi-restraints excluded: chain V residue 121 VAL Chi-restraints excluded: chain V residue 160 LEU Chi-restraints excluded: chain V residue 169 SER Chi-restraints excluded: chain W residue 21 THR Chi-restraints excluded: chain W residue 32 SER Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 58 LEU Chi-restraints excluded: chain W residue 81 ARG Chi-restraints excluded: chain W residue 94 ILE Chi-restraints excluded: chain W residue 105 VAL Chi-restraints excluded: chain W residue 110 LEU Chi-restraints excluded: chain W residue 120 ASP Chi-restraints excluded: chain W residue 125 VAL Chi-restraints excluded: chain W residue 169 SER Chi-restraints excluded: chain X residue 41 ILE Chi-restraints excluded: chain X residue 55 LEU Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 77 GLU Chi-restraints excluded: chain X residue 121 CYS Chi-restraints excluded: chain X residue 145 MET Chi-restraints excluded: chain X residue 152 LEU Chi-restraints excluded: chain X residue 174 VAL Chi-restraints excluded: chain X residue 192 ASP Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain Y residue 53 THR Chi-restraints excluded: chain Y residue 64 VAL Chi-restraints excluded: chain Y residue 73 TYR Chi-restraints excluded: chain Y residue 121 LEU Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 45 MET Chi-restraints excluded: chain Z residue 51 ASP Chi-restraints excluded: chain Z residue 74 ILE Chi-restraints excluded: chain Z residue 87 VAL Chi-restraints excluded: chain Z residue 89 GLN Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain Z residue 125 THR Chi-restraints excluded: chain Z residue 138 VAL Chi-restraints excluded: chain a residue 22 ILE Chi-restraints excluded: chain a residue 29 LEU Chi-restraints excluded: chain a residue 35 ILE Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain a residue 67 ILE Chi-restraints excluded: chain a residue 71 ARG Chi-restraints excluded: chain a residue 133 ASP Chi-restraints excluded: chain a residue 175 VAL Chi-restraints excluded: chain b residue 26 MET Chi-restraints excluded: chain b residue 42 ILE Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 88 ILE Chi-restraints excluded: chain b residue 112 ILE Chi-restraints excluded: chain b residue 130 VAL Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 159 VAL Chi-restraints excluded: chain b residue 169 VAL Chi-restraints excluded: chain b residue 186 ARG Chi-restraints excluded: chain b residue 189 ILE Chi-restraints excluded: chain b residue 191 THR Chi-restraints excluded: chain b residue 193 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 342 optimal weight: 3.9990 chunk 538 optimal weight: 5.9990 chunk 269 optimal weight: 0.1980 chunk 231 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 470 optimal weight: 7.9990 chunk 291 optimal weight: 9.9990 chunk 344 optimal weight: 0.9980 chunk 132 optimal weight: 10.0000 chunk 462 optimal weight: 3.9990 chunk 140 optimal weight: 0.5980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 24 GLN ** C 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 GLN ** D 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** E 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 22 GLN ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 187 HIS K 82 ASN K 87 ASN ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 GLN M 80 ASN N 104 ASN ** O 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 54 GLN ** R 154 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 187 HIS ** Z 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 162 GLN a 77 HIS a 80 ASN b 61 GLN b 104 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.193925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4231 r_free = 0.4231 target = 0.188683 restraints weight = 71729.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.190027 restraints weight = 43105.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.190974 restraints weight = 28568.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.191615 restraints weight = 19883.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.192043 restraints weight = 14517.799| |-----------------------------------------------------------------------------| r_work (final): 0.4269 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6357 moved from start: 0.5385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 44190 Z= 0.150 Angle : 0.724 14.125 59626 Z= 0.372 Chirality : 0.046 0.262 6732 Planarity : 0.006 0.109 7614 Dihedral : 6.433 57.612 6130 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 16.56 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.20 % Favored : 95.67 % Rotamer: Outliers : 5.23 % Allowed : 25.98 % Favored : 68.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.96 (0.11), residues: 5432 helix: -0.38 (0.11), residues: 1952 sheet: -2.17 (0.14), residues: 1248 loop : -1.43 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG Z 120 TYR 0.032 0.002 TYR H 90 PHE 0.029 0.002 PHE Z 54 TRP 0.021 0.002 TRP J 153 HIS 0.010 0.001 HIS Q 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (44174) covalent geometry : angle 0.72407 / 0.37 (59622) SS BOND : bond 0.00039 / 0.02 ( 2) SS BOND : angle 1.60965 / 1.00 ( 4) hydrogen bonds : bond 0.04254 / 2.78 ( 1202) hydrogen bonds : angle 4.62759 / 3.23 ( 3606) Misc. bond : bond 0.00293 / 0.15 ( 14) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1553 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 241 poor density : 1312 time to evaluate : 1.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU E 236 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU M 205 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU S 236 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU a 205 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: B 70 HIS cc_start: 0.5369 (OUTLIER) cc_final: 0.4451 (p90) REVERT: B 102 GLU cc_start: 0.6702 (OUTLIER) cc_final: 0.6413 (pm20) REVERT: B 165 ASN cc_start: 0.6760 (t0) cc_final: 0.6446 (t0) REVERT: C 12 PHE cc_start: 0.7450 (OUTLIER) cc_final: 0.7109 (m-80) REVERT: C 119 GLN cc_start: 0.6116 (tp-100) cc_final: 0.5864 (tp-100) REVERT: D 153 TYR cc_start: 0.7616 (p90) cc_final: 0.7296 (p90) REVERT: E 86 LYS cc_start: 0.7434 (ttpt) cc_final: 0.6856 (mtpt) REVERT: E 189 MET cc_start: 0.3366 (OUTLIER) cc_final: 0.2559 (tpp) REVERT: F 125 ARG cc_start: 0.5625 (mmt180) cc_final: 0.5377 (mmt90) REVERT: H 103 TRP cc_start: 0.5825 (OUTLIER) cc_final: 0.4743 (t60) REVERT: H 164 MET cc_start: 0.5299 (OUTLIER) cc_final: 0.4464 (ptt) REVERT: I 30 ASN cc_start: 0.7617 (t0) cc_final: 0.7141 (t0) REVERT: I 203 ARG cc_start: 0.4974 (mmt90) cc_final: 0.4007 (mmt-90) REVERT: J 93 LEU cc_start: 0.7742 (tp) cc_final: 0.7442 (tt) REVERT: L 74 ILE cc_start: 0.7372 (OUTLIER) cc_final: 0.7038 (tt) REVERT: M 28 ARG cc_start: 0.5942 (ptt180) cc_final: 0.5006 (ptm160) REVERT: M 66 LYS cc_start: 0.8387 (mtmm) cc_final: 0.8073 (mtmm) REVERT: N 76 LEU cc_start: 0.6364 (OUTLIER) cc_final: 0.6029 (pp) REVERT: N 86 ARG cc_start: 0.7329 (mmt-90) cc_final: 0.6871 (mmm160) REVERT: N 90 SER cc_start: 0.8139 (OUTLIER) cc_final: 0.7812 (m) REVERT: N 186 ARG cc_start: 0.4035 (OUTLIER) cc_final: 0.3691 (tpm170) REVERT: P 70 HIS cc_start: 0.5345 (OUTLIER) cc_final: 0.4401 (p90) REVERT: P 102 GLU cc_start: 0.6698 (OUTLIER) cc_final: 0.6413 (pm20) REVERT: P 165 ASN cc_start: 0.6757 (t0) cc_final: 0.6429 (t0) REVERT: Q 4 ARG cc_start: 0.4859 (mtp-110) cc_final: 0.4408 (mtm110) REVERT: Q 12 PHE cc_start: 0.7436 (OUTLIER) cc_final: 0.7117 (m-80) REVERT: R 153 TYR cc_start: 0.7671 (p90) cc_final: 0.7371 (p90) REVERT: S 189 MET cc_start: 0.3322 (OUTLIER) cc_final: 0.2576 (tpp) REVERT: T 18 ARG cc_start: 0.5433 (mpp-170) cc_final: 0.4889 (mpt90) REVERT: T 125 ARG cc_start: 0.5705 (mmt180) cc_final: 0.5462 (mmt90) REVERT: U 167 LYS cc_start: 0.6701 (OUTLIER) cc_final: 0.6394 (pttt) REVERT: W 203 ARG cc_start: 0.5078 (mmt90) cc_final: 0.4048 (mmt-90) REVERT: Z 74 ILE cc_start: 0.7472 (OUTLIER) cc_final: 0.7085 (tt) REVERT: Z 81 LYS cc_start: 0.8202 (tppt) cc_final: 0.7757 (mttt) REVERT: a 28 ARG cc_start: 0.5912 (ptt180) cc_final: 0.5059 (ptm160) REVERT: a 66 LYS cc_start: 0.8402 (mtmm) cc_final: 0.8157 (mtmm) REVERT: a 71 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.6647 (mtp180) REVERT: a 173 ARG cc_start: 0.5516 (tpp-160) cc_final: 0.4827 (mtp85) REVERT: b 5 MET cc_start: 0.6104 (mmt) cc_final: 0.5817 (mmt) REVERT: b 76 LEU cc_start: 0.6327 (OUTLIER) cc_final: 0.5994 (pp) REVERT: b 86 ARG cc_start: 0.7308 (mmt-90) cc_final: 0.7077 (mmm160) REVERT: b 186 ARG cc_start: 0.4031 (OUTLIER) cc_final: 0.3677 (tpm170) outliers start: 241 outliers final: 180 residues processed: 1454 average time/residue: 0.2770 time to fit residues: 649.0939 Evaluate side-chains 1440 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 199 poor density : 1241 time to evaluate : 1.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 104 VAL Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain D residue 210 VAL Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 189 MET Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 213 THR Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain F residue 35 THR Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 174 ARG Chi-restraints excluded: chain G residue 22 GLN Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain G residue 133 CYS Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 98 ILE Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 81 ARG Chi-restraints excluded: chain I residue 83 LEU Chi-restraints excluded: chain I residue 120 ASP Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 70 LEU Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 121 CYS Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 192 ASP Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 44 LEU Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 51 ASP Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 88 ILE Chi-restraints excluded: chain N residue 90 SER Chi-restraints excluded: chain N residue 104 ASN Chi-restraints excluded: chain N residue 112 ILE Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 186 ARG Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain O residue 76 ILE Chi-restraints excluded: chain O residue 84 THR Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 159 TYR Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 207 SER Chi-restraints excluded: chain P residue 47 THR Chi-restraints excluded: chain P residue 70 HIS Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain P residue 133 LEU Chi-restraints excluded: chain Q residue 12 PHE Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 100 GLN Chi-restraints excluded: chain Q residue 155 ASN Chi-restraints excluded: chain Q residue 203 VAL Chi-restraints excluded: chain Q residue 224 VAL Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 141 THR Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 167 SER Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain S residue 28 ILE Chi-restraints excluded: chain S residue 38 ILE Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 153 LEU Chi-restraints excluded: chain S residue 161 THR Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 189 MET Chi-restraints excluded: chain S residue 191 LEU Chi-restraints excluded: chain S residue 213 THR Chi-restraints excluded: chain S residue 215 ILE Chi-restraints excluded: chain S residue 220 VAL Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain T residue 35 THR Chi-restraints excluded: chain T residue 47 VAL Chi-restraints excluded: chain U residue 50 GLU Chi-restraints excluded: chain U residue 70 ASP Chi-restraints excluded: chain U residue 90 ILE Chi-restraints excluded: chain U residue 133 CYS Chi-restraints excluded: chain U residue 167 LYS Chi-restraints excluded: chain U residue 219 LEU Chi-restraints excluded: chain V residue 6 VAL Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 103 TRP Chi-restraints excluded: chain V residue 121 VAL Chi-restraints excluded: chain V residue 169 SER Chi-restraints excluded: chain W residue 32 SER Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 58 LEU Chi-restraints excluded: chain W residue 81 ARG Chi-restraints excluded: chain W residue 83 LEU Chi-restraints excluded: chain W residue 110 LEU Chi-restraints excluded: chain W residue 125 VAL Chi-restraints excluded: chain W residue 169 SER Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 65 ARG Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 77 GLU Chi-restraints excluded: chain X residue 121 CYS Chi-restraints excluded: chain X residue 152 LEU Chi-restraints excluded: chain X residue 174 VAL Chi-restraints excluded: chain X residue 192 ASP Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain Y residue 53 THR Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 74 ILE Chi-restraints excluded: chain Z residue 87 VAL Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain Z residue 125 THR Chi-restraints excluded: chain a residue 22 ILE Chi-restraints excluded: chain a residue 29 LEU Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain a residue 67 ILE Chi-restraints excluded: chain a residue 71 ARG Chi-restraints excluded: chain a residue 175 VAL Chi-restraints excluded: chain b residue 26 MET Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 88 ILE Chi-restraints excluded: chain b residue 104 ASN Chi-restraints excluded: chain b residue 112 ILE Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 169 VAL Chi-restraints excluded: chain b residue 186 ARG Chi-restraints excluded: chain b residue 189 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 132 optimal weight: 5.9990 chunk 450 optimal weight: 8.9990 chunk 22 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 chunk 444 optimal weight: 0.9990 chunk 537 optimal weight: 0.0030 chunk 470 optimal weight: 3.9990 chunk 234 optimal weight: 10.0000 chunk 166 optimal weight: 20.0000 chunk 2 optimal weight: 0.3980 overall best weight: 1.2794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 23 GLN ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** E 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 HIS ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 GLN K 24 ASN K 87 ASN ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 GLN N 104 ASN O 24 GLN ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 6 ASN Y 82 ASN ** Z 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 162 GLN a 77 HIS b 104 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.196252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.190863 restraints weight = 71781.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.192292 restraints weight = 44263.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4279 r_free = 0.4279 target = 0.193281 restraints weight = 29159.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.193940 restraints weight = 20380.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.194373 restraints weight = 14751.795| |-----------------------------------------------------------------------------| r_work (final): 0.4292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6313 moved from start: 0.5597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 44190 Z= 0.142 Angle : 0.730 13.892 59626 Z= 0.376 Chirality : 0.046 0.229 6732 Planarity : 0.006 0.093 7614 Dihedral : 6.264 56.753 6130 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 16.37 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.20 % Favored : 95.67 % Rotamer: Outliers : 4.29 % Allowed : 27.56 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.11), residues: 5432 helix: -0.23 (0.11), residues: 1952 sheet: -2.08 (0.14), residues: 1248 loop : -1.32 (0.13), residues: 2232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG G 114 TYR 0.041 0.002 TYR L 88 PHE 0.032 0.002 PHE F 87 TRP 0.028 0.002 TRP N 107 HIS 0.010 0.001 HIS Q 240 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (44174) covalent geometry : angle 0.73006 / 0.38 (59622) SS BOND : bond 0.00151 / 0.08 ( 2) SS BOND : angle 1.36063 / 0.83 ( 4) hydrogen bonds : bond 0.04199 / 2.76 ( 1202) hydrogen bonds : angle 4.54296 / 3.17 ( 3606) Misc. bond : bond 0.00279 / 0.14 ( 14) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10864 Ramachandran restraints generated. 5432 Oldfield, 0 Emsley, 5432 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1495 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 198 poor density : 1297 time to evaluate : 1.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU E 236 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU M 205 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU S 236 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "GLU a 205 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash REVERT: A 76 ILE cc_start: 0.7337 (OUTLIER) cc_final: 0.6520 (mp) REVERT: B 70 HIS cc_start: 0.5318 (OUTLIER) cc_final: 0.4455 (p90) REVERT: B 102 GLU cc_start: 0.6640 (OUTLIER) cc_final: 0.6362 (pm20) REVERT: B 165 ASN cc_start: 0.6640 (t0) cc_final: 0.6388 (t0) REVERT: C 12 PHE cc_start: 0.7271 (OUTLIER) cc_final: 0.6950 (m-80) REVERT: C 48 GLU cc_start: 0.6057 (OUTLIER) cc_final: 0.5685 (tp30) REVERT: D 153 TYR cc_start: 0.7574 (p90) cc_final: 0.7356 (p90) REVERT: D 233 GLU cc_start: 0.4953 (mt-10) cc_final: 0.4436 (mm-30) REVERT: E 86 LYS cc_start: 0.7383 (ttpt) cc_final: 0.6791 (mtpt) REVERT: E 187 LYS cc_start: 0.5922 (mmtm) cc_final: 0.4908 (mmmt) REVERT: F 180 MET cc_start: 0.5506 (tpp) cc_final: 0.4894 (mpp) REVERT: H 103 TRP cc_start: 0.5692 (OUTLIER) cc_final: 0.4631 (t60) REVERT: H 164 MET cc_start: 0.5313 (OUTLIER) cc_final: 0.4481 (ptt) REVERT: I 30 ASN cc_start: 0.7554 (t0) cc_final: 0.7118 (t0) REVERT: I 203 ARG cc_start: 0.4777 (mmt90) cc_final: 0.3836 (mmt-90) REVERT: J 82 LYS cc_start: 0.4285 (tppt) cc_final: 0.3755 (mtpp) REVERT: J 93 LEU cc_start: 0.7742 (tp) cc_final: 0.7526 (tt) REVERT: L 74 ILE cc_start: 0.7389 (OUTLIER) cc_final: 0.6983 (tt) REVERT: L 140 ASP cc_start: 0.5662 (m-30) cc_final: 0.5176 (m-30) REVERT: M 28 ARG cc_start: 0.6020 (ptt180) cc_final: 0.5141 (ptm160) REVERT: M 66 LYS cc_start: 0.8331 (mtmm) cc_final: 0.7973 (mtmm) REVERT: M 168 LEU cc_start: 0.5621 (mp) cc_final: 0.4462 (tp) REVERT: N 76 LEU cc_start: 0.6310 (OUTLIER) cc_final: 0.6022 (pp) REVERT: N 186 ARG cc_start: 0.4173 (OUTLIER) cc_final: 0.1525 (tpm170) REVERT: P 70 HIS cc_start: 0.5294 (OUTLIER) cc_final: 0.4412 (p90) REVERT: P 102 GLU cc_start: 0.6644 (OUTLIER) cc_final: 0.6377 (pm20) REVERT: P 165 ASN cc_start: 0.6616 (t0) cc_final: 0.6352 (t0) REVERT: Q 12 PHE cc_start: 0.7269 (OUTLIER) cc_final: 0.6952 (m-80) REVERT: R 153 TYR cc_start: 0.7599 (p90) cc_final: 0.7234 (p90) REVERT: S 187 LYS cc_start: 0.6102 (mmtm) cc_final: 0.5159 (mmmt) REVERT: S 189 MET cc_start: 0.3352 (OUTLIER) cc_final: 0.2511 (tpp) REVERT: T 18 ARG cc_start: 0.5371 (mpp-170) cc_final: 0.4818 (mpt90) REVERT: T 180 MET cc_start: 0.5516 (tpp) cc_final: 0.4888 (mpp) REVERT: U 167 LYS cc_start: 0.6728 (OUTLIER) cc_final: 0.6311 (pttt) REVERT: W 30 ASN cc_start: 0.7556 (t0) cc_final: 0.7109 (t0) REVERT: W 203 ARG cc_start: 0.4868 (mmt90) cc_final: 0.3916 (mmt-90) REVERT: X 82 LYS cc_start: 0.4442 (mmtp) cc_final: 0.4124 (mtpp) REVERT: Y 41 LYS cc_start: 0.5496 (mptt) cc_final: 0.4961 (mptt) REVERT: Z 74 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.6951 (tt) REVERT: Z 140 ASP cc_start: 0.5925 (m-30) cc_final: 0.5371 (m-30) REVERT: a 28 ARG cc_start: 0.6028 (ptt180) cc_final: 0.5161 (ptm160) REVERT: a 173 ARG cc_start: 0.5527 (tpp-160) cc_final: 0.4736 (mtp85) REVERT: b 76 LEU cc_start: 0.6292 (OUTLIER) cc_final: 0.5982 (pp) REVERT: b 86 ARG cc_start: 0.7285 (mmt-90) cc_final: 0.7076 (mmm160) REVERT: b 186 ARG cc_start: 0.4150 (OUTLIER) cc_final: 0.1475 (tpm170) outliers start: 198 outliers final: 153 residues processed: 1413 average time/residue: 0.2898 time to fit residues: 658.3416 Evaluate side-chains 1415 residues out of total 4612 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 171 poor density : 1244 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 ILE Chi-restraints excluded: chain A residue 84 THR Chi-restraints excluded: chain A residue 113 MET Chi-restraints excluded: chain A residue 159 TYR Chi-restraints excluded: chain A residue 177 SER Chi-restraints excluded: chain A residue 207 SER Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 70 HIS Chi-restraints excluded: chain B residue 102 GLU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 133 LEU Chi-restraints excluded: chain C residue 12 PHE Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 48 GLU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 100 GLN Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 203 VAL Chi-restraints excluded: chain C residue 224 VAL Chi-restraints excluded: chain D residue 39 ASP Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 150 SER Chi-restraints excluded: chain D residue 152 THR Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain D residue 208 LEU Chi-restraints excluded: chain E residue 38 ILE Chi-restraints excluded: chain E residue 64 ILE Chi-restraints excluded: chain E residue 68 VAL Chi-restraints excluded: chain E residue 79 SER Chi-restraints excluded: chain E residue 121 LEU Chi-restraints excluded: chain E residue 153 LEU Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 163 VAL Chi-restraints excluded: chain E residue 191 LEU Chi-restraints excluded: chain E residue 215 ILE Chi-restraints excluded: chain E residue 220 VAL Chi-restraints excluded: chain E residue 236 GLU Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain G residue 50 GLU Chi-restraints excluded: chain G residue 70 ASP Chi-restraints excluded: chain G residue 90 ILE Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 103 TRP Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 164 MET Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 37 ILE Chi-restraints excluded: chain I residue 52 THR Chi-restraints excluded: chain I residue 58 LEU Chi-restraints excluded: chain I residue 81 ARG Chi-restraints excluded: chain I residue 120 ASP Chi-restraints excluded: chain I residue 125 VAL Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain J residue 57 THR Chi-restraints excluded: chain J residue 70 LEU Chi-restraints excluded: chain J residue 77 GLU Chi-restraints excluded: chain J residue 174 VAL Chi-restraints excluded: chain J residue 192 ASP Chi-restraints excluded: chain K residue 17 SER Chi-restraints excluded: chain K residue 20 VAL Chi-restraints excluded: chain K residue 53 THR Chi-restraints excluded: chain K residue 167 LEU Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 87 VAL Chi-restraints excluded: chain L residue 102 CYS Chi-restraints excluded: chain L residue 125 THR Chi-restraints excluded: chain M residue 22 ILE Chi-restraints excluded: chain M residue 55 SER Chi-restraints excluded: chain M residue 67 ILE Chi-restraints excluded: chain M residue 175 VAL Chi-restraints excluded: chain N residue 26 MET Chi-restraints excluded: chain N residue 76 LEU Chi-restraints excluded: chain N residue 88 ILE Chi-restraints excluded: chain N residue 90 SER Chi-restraints excluded: chain N residue 104 ASN Chi-restraints excluded: chain N residue 112 ILE Chi-restraints excluded: chain N residue 169 VAL Chi-restraints excluded: chain N residue 186 ARG Chi-restraints excluded: chain N residue 189 ILE Chi-restraints excluded: chain O residue 84 THR Chi-restraints excluded: chain O residue 113 MET Chi-restraints excluded: chain O residue 159 TYR Chi-restraints excluded: chain O residue 177 SER Chi-restraints excluded: chain O residue 207 SER Chi-restraints excluded: chain P residue 70 HIS Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 131 VAL Chi-restraints excluded: chain P residue 133 LEU Chi-restraints excluded: chain Q residue 12 PHE Chi-restraints excluded: chain Q residue 25 MET Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 92 LEU Chi-restraints excluded: chain Q residue 100 GLN Chi-restraints excluded: chain Q residue 155 ASN Chi-restraints excluded: chain Q residue 203 VAL Chi-restraints excluded: chain Q residue 224 VAL Chi-restraints excluded: chain R residue 39 ASP Chi-restraints excluded: chain R residue 77 THR Chi-restraints excluded: chain R residue 104 VAL Chi-restraints excluded: chain R residue 141 THR Chi-restraints excluded: chain R residue 150 SER Chi-restraints excluded: chain R residue 152 THR Chi-restraints excluded: chain R residue 167 SER Chi-restraints excluded: chain R residue 168 VAL Chi-restraints excluded: chain R residue 199 VAL Chi-restraints excluded: chain R residue 208 LEU Chi-restraints excluded: chain R residue 210 VAL Chi-restraints excluded: chain S residue 38 ILE Chi-restraints excluded: chain S residue 64 ILE Chi-restraints excluded: chain S residue 68 VAL Chi-restraints excluded: chain S residue 79 SER Chi-restraints excluded: chain S residue 121 LEU Chi-restraints excluded: chain S residue 153 LEU Chi-restraints excluded: chain S residue 161 THR Chi-restraints excluded: chain S residue 163 VAL Chi-restraints excluded: chain S residue 189 MET Chi-restraints excluded: chain S residue 191 LEU Chi-restraints excluded: chain S residue 215 ILE Chi-restraints excluded: chain S residue 220 VAL Chi-restraints excluded: chain S residue 236 GLU Chi-restraints excluded: chain T residue 47 VAL Chi-restraints excluded: chain U residue 50 GLU Chi-restraints excluded: chain U residue 70 ASP Chi-restraints excluded: chain U residue 90 ILE Chi-restraints excluded: chain U residue 167 LYS Chi-restraints excluded: chain V residue 6 VAL Chi-restraints excluded: chain V residue 21 THR Chi-restraints excluded: chain V residue 22 THR Chi-restraints excluded: chain V residue 52 THR Chi-restraints excluded: chain V residue 103 TRP Chi-restraints excluded: chain V residue 121 VAL Chi-restraints excluded: chain V residue 169 SER Chi-restraints excluded: chain W residue 37 ILE Chi-restraints excluded: chain W residue 52 THR Chi-restraints excluded: chain W residue 58 LEU Chi-restraints excluded: chain W residue 81 ARG Chi-restraints excluded: chain W residue 110 LEU Chi-restraints excluded: chain X residue 57 THR Chi-restraints excluded: chain X residue 65 ARG Chi-restraints excluded: chain X residue 70 LEU Chi-restraints excluded: chain X residue 77 GLU Chi-restraints excluded: chain X residue 174 VAL Chi-restraints excluded: chain X residue 192 ASP Chi-restraints excluded: chain Y residue 17 SER Chi-restraints excluded: chain Y residue 20 VAL Chi-restraints excluded: chain Y residue 44 LEU Chi-restraints excluded: chain Y residue 53 THR Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 59 LEU Chi-restraints excluded: chain Z residue 74 ILE Chi-restraints excluded: chain Z residue 87 VAL Chi-restraints excluded: chain Z residue 102 CYS Chi-restraints excluded: chain Z residue 125 THR Chi-restraints excluded: chain a residue 22 ILE Chi-restraints excluded: chain a residue 55 SER Chi-restraints excluded: chain a residue 67 ILE Chi-restraints excluded: chain a residue 175 VAL Chi-restraints excluded: chain b residue 26 MET Chi-restraints excluded: chain b residue 76 LEU Chi-restraints excluded: chain b residue 88 ILE Chi-restraints excluded: chain b residue 104 ASN Chi-restraints excluded: chain b residue 112 ILE Chi-restraints excluded: chain b residue 145 LEU Chi-restraints excluded: chain b residue 169 VAL Chi-restraints excluded: chain b residue 186 ARG Chi-restraints excluded: chain b residue 189 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 544 random chunks: chunk 11 optimal weight: 3.9990 chunk 450 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 152 optimal weight: 0.7980 chunk 454 optimal weight: 2.9990 chunk 135 optimal weight: 6.9990 chunk 287 optimal weight: 2.9990 chunk 90 optimal weight: 10.0000 chunk 74 optimal weight: 0.0370 chunk 478 optimal weight: 10.0000 overall best weight: 1.9664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 104 ASN ** E 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 225 ASN ** H 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 36 HIS ** N 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 33 ASN ** P 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 118 GLN ** Q 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 240 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 224 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 225 ASN U 110 HIS ** V 38 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 85 GLN Z 62 GLN ** Z 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 77 HIS ** b 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.196040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.190774 restraints weight = 72300.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.192164 restraints weight = 45238.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.193080 restraints weight = 30606.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.193712 restraints weight = 21806.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.194157 restraints weight = 16085.121| |-----------------------------------------------------------------------------| r_work (final): 0.4287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6322 moved from start: 0.5689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 44190 Z= 0.150 Angle : 0.735 13.618 59626 Z= 0.376 Chirality : 0.047 0.234 6732 Planarity : 0.006 0.096 7614 Dihedral : 6.226 56.100 6130 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 16.52 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.20 % Favored : 95.67 % Rotamer: Outliers : 4.29 % Allowed : 27.56 % Favored : 68.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.11), residues: 5432 helix: -0.20 (0.11), residues: 1944 sheet: -2.03 (0.14), residues: 1246 loop : -1.27 (0.13), residues: 2242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG G 114 TYR 0.034 0.002 TYR V 90 PHE 0.034 0.002 PHE T 97 TRP 0.029 0.002 TRP N 107 HIS 0.011 0.001 HIS H 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (44174) covalent geometry : angle 0.73458 / 0.38 (59622) SS BOND : bond 0.00232 / 0.12 ( 2) SS BOND : angle 1.28532 / 0.75 ( 4) hydrogen bonds : bond 0.04156 / 2.71 ( 1202) hydrogen bonds : angle 4.53280 / 3.16 ( 3606) Misc. bond : bond 0.00280 / 0.14 ( 14) =============================================================================== Job complete usr+sys time: 10739.65 seconds wall clock time: 185 minutes 13.83 seconds (11113.83 seconds total)